Yes, a haunt shift spell can translate a slaymate into a haunting presence that's tied to an object that the caster can carry, but it's not guaranteed

Before committing to this idea, clear with the DM that the campaign uses the Variant Rule: Haunting Presences. Not all DMs use all variant rules, so it's possible that haunting presences—and by extension the the 5th-level Sor/Wis spell haunt shift [necro] (Libris Mortis 66–7)—won't exist. If they don't, you'll have to find a more traditional way to tote around your slaymate (122–3) on your adventures.

Even if haunting presences do exist, the DM may rule that the DM not the caster picks to what or where the haunt shift spell ties the slaymate:

Whenever an undead appears as a haunting presence, it haunts an unattended, mundane object or location. Using the same decision-making process that he uses to populate a location or area with a standard monster, the DM simply chooses an unattended mundane object or location as the subject of a haunting presence.… An undead may haunt a discrete object of at least Tiny size and no larger than Huge size. Items… in the possession of a character… cannot be haunted.… A haunting presence becomes a part of the object or location haunted. (6 and emphasis mine)

The haunt shift spell doesn't create a new creature but translates the existing undead creature into a haunting presence, so the DM decides to what or to where a haunting presence is tied. Thus a haunt shift spell is just as likely to tie that translated slaymate to the chandelier, area rug, dining table, or the ritual casting room itself as it is to tie it to the amulet, dagger, ring, scarf, or whatever you'd prefer. Consider paying for pizza before casting the spell.

Finally, slaymates come about "when a guardian's betrayal, either outright or through negligence, leads to death" (122). In case it's not obvious: Slaymates are dead abused children. Yeah. So. Um. There's baggage there, and some folks might be playing role-playing games to escape these issues. Consider clearing the slaymate with your group as well as the DM. Everyone having fun at the table is more important than your PC's reduced metamagic costs.¹

Anyway. Sorry. Back to mechanics.

Yes, most of the metamagic feats apply as the question describes if the DM rules that metamagic feats are applied sequentially in the creature's preferred order

You want to prepare (or cast without preparation) a spell that's modified by a metamagic feat then by another metamagic feat then by a third then by maybe a dozen more, with all the modification applying in the order of your choosing. Specifically, you want the next modification must see the spell as already having been modified by previous modifications. This is a popular position, and it's supported by the Main FAQ with this exchange:

When do "add-on" effects such as poison occur? For example, if an assassin delivers a death attack with a weapon bearing wyvern poison, does the poison take effect first, thus potentially reducing the target’s Fortitude save against the death attack?

As a general guideline, whenever the rules don’t stipulate an order of operations for special effects (such as spells or special abilities), you should apply them in the order that’s most beneficial to the "controller" of the effect.… (51).

The rules don't stipulate an order of operations for modifying a spell with metamagic feats, therefore you can apply them in the order that's best for you. This kind of sequential metamagic makes sense, it's easy, and it's fun. (You can't make a locate city bomb without sequential metamagic, for instance.)

The less popular position usually goes something like this: "During preparation, the character chooses which spells to prepare with metamagic feats" (Player's Handbook 88), and that's pretty much the last word on preparing spells with metamagic feats. (Similar statements are made about casting without preparation, they not adding anything either.) Thus, as no order is mentioned, there is no order. Instead, all metamagic feats modify the spell simultaneously, all modifying the spell according to their own rules, and none of the modifications interacting with each other.

This kind of simultaneous metamagic is messy. It requires figuring out how each modification applies to a spell but not to additional effects due to the spell having been affected by other modifications. This position is predicated on how metamagic feats interact according to the Player's Handbook. That may sound authoritative initially, but it's only mentioned once and in passing:

An empowered, maximized spell gains the separate benefits of each feat: the maximum result plus one-half the normally rolled result. An empowered, maximized fireball cast by a 15th-level wizard deals points of damage equal to 60 plus one half of 10d6. (98)

Thus to get the most woosh from your fireball spell you'd modify it with the feat Empower Spell (PH 93) first and then with the feat Maximize Spell (PH 97–8) so that your fireball spell deals 90 points of damage. The Player's Handbook says that's not how this combination of modifications work; instead, the empowering modification just doesn't interact with the maximizing modification. The Player's Handbook here uses simultaneous metamagic.

The counterarguments to simultaneous metamagic are legion. The main one is that this interaction is unique to these two feats. However, there're no other metamagic feats in the Player's Handbook that can be used as examples of this interaction, and the core rules are designed to stand alone. Another argument comes from 3.5 architect Andy Collins in the Dragon #340 Sage Advice column "Official Answers to Your Questions" (83) that's repeated in the Main FAQ (37) and below:

If my wizard applies Energy Admixture… and Maximize Spell to the same spell, does he get a spell that deals double its maximized damage (maximum normal damage in two different energy types)? If he also applied the Twin Spell feat… to the same spell would it duplicate the entire effect?

Yes and yes. Assuming your character can cast 13th-level spells—the slot required by a 2nd-level spell affected by these metamagic feats—a scorching ray so affected would create two sets of three rays each, with each ray dealing 24 points of fire damage (4d6, maximized) and 24 points of a second energy type (as appropriate for your Energy Substitution feat), for a grand total of 288 points of damage… assuming all six rays hit their target.

According to simultaneous metamagic, the feats Maximize Spell, Energy Admixture (cold) (Complete Arcane 78), and Twin Spell (84) could instead result in a scorching ray spell that launches 3 rays that each deal both 24 points of fire damage and 4d6 points of cold damage and also launches another 3 rays that each deal 4d6 points of fire damage. (That's an average of 156 points of damage—lousy for a 13th-level spell.) Collins, though, says that's not how this combination of modifications work; he's using sequential metamagic, and so far as I'm aware that position is officially uncontested except by the Player's Hanbook's example. I get the sense that the simultaneous metamagic folks are largely voices in the wilderness. That doesn't mean they don't exist, though, and your DM could be one.²

On the Fell Frighten feat

The benefit of the metamagic feat Fell Frighten (LM 27), in part, says, "You can alter a spell that deals damage to foes so that any creature subject to fear effects and mind-affecting spells and abilities that is dealt damage also becomes shaken for 1 minute." To rephrase: a creature that is dealt damage by a spell modified by the Fell Frighten feat is shaken for 1 min. if the creature can be affected by both fear effects and mind affecting spells and abilities. Nothing in the feat's description says that the spell that's modified by the Fell Frighten feat actually gains the descriptor mind-affecting (PH 174).

The case can be made that because the modified spell creates an effect that causes a fear condition then the modified spell is a fear attack therefore the spell is a mind-affecting spell because fear attacks are always mind-affecting (Monster Manual 309 and Rules Compendium 53). However, the feat's benefit already spells out exactly what it does in a way that's pretty clear by 3.5 standards, so may your DM be open-minded.

On the improved metamagic ability

The incantatrix level 10 class feature improved metamagic, a supernatural ability, in part, says, that "whenever [an incantatrix] uses a metamagic feat, the required increase in spell level (if any) is reduced by one (minimum +1 spell level)" (Player's Guide to Faerûn 63). That minimum +1 may be an impossibly hard floor. A DM could ask, "Are you benefiting from the ability?" and when you say, "Yes," then the DM says, "Then the minimum spell level for any spell to which you've applied that ability is +1." That's pretty serious—probably serious enough to make some folks leave that table—, but it's a ruling that can be made. I suspect, though, that most folks view that minimum +1 as applying to the improved metamagic ability itself and let other game elements disregard it.

On the pale aura ability

While within the supernatural ability pale aura that's generated by a slaymate (or by its haunting presence), a caster that "uses a metamagic feat on a spell from the school of necromancy can prepare or use the spell as if it took up a spell slot one level lower than what the metamagic necromancy spell would normally require" (LM 123). There are at least two ways the DM can rule on this:

• Sequential metamagic: Each metamagic feat modifying a spell of the necromancy school reduces that spell's spell level by −1, cumulatively.
• Simultaneous metamagic: One or more metamagic feats modifying a spell of the necromancy school reduce that spell's spell level by a −1, noncumulatively.

For example, sequential metamagic has a necromancer apply the metamagic feats Alternative Source Spell (Dragon #325 61), Black Lore of Moil (CAr 75–6), Invisible Spell (Cityscape 61), Quicken Spell (PH 98), and Sanctum Spell (CAr 82-3) separately to the 4th-level spell enervation [necro] (PH 226) so that modified enervation spell is prepared (or cast without preparation) as a 3rd-level spell. Simultaneous metamagic would instead have that same modified spell be prepared (or cast without preparation) as a 7th-level spell.

All this in a big pile

Because there are so many variables I'll address but two scenarios.

• Best case scenario: Sequential metamagic is a go, and everything works. In order, you modify the 2nd-level Sor/Wiz spell scorching ray [evoc] (PH 274) with the Fell Frighten feat so that it's a mind-affecting scorching ray spell. Then you modify that mind-affecting scorching ray spell with the Song of the Dead feat so that it's a mind-affecting scorching ray spell of the necromancy school. Then you apply the benefit of the incantatrix's improved metamagic ability to each feat's spell level adjustments (still bound by the minimum +1 language). Then you apply to that a mind-affecting scorching ray spell of the necromancy school that's presently a 4th-level spell the benefit of the slaymate's pale aura ability to both feat's spell level adjustments separately. You end up preparing that fell frightening deadsong scorching ray spell as a 2nd-level spell. Modifying the spell with additional metamagic feats sees that spell's spell level reduced by −2 per metamagic modification with no spell level floor.

• Worst case scenario: Simultaneous metamagic is used, and nothing works. You can apply the Fell Frighten feat to your sorching ray spell, but even if the Fell Frighten feat were to add the mind-affecting descriptor to that scorching ray spell, it wouldn't see that descriptor before you attempted to modify the spell with the Song of the Dead feat, so the Song of the Dead feat just can't be applied. The Fell Frighten feat's spell level adjustment is still affected by the improved metamagic ability normally, but the slaymate's pale aura ability doesn't lower that scorching ray spell's spell level further because that scorching ray isn't a necromancy spell. You prepare that fell frightening scorching ray spell as a 3rd-level spell.

As you can see, these are wildly different campaigns for the purveyor of metamagic, and there're many shades in between. However, even in the best case scenario, for all the rigmarole, this combination won't break many campaign. Some other combinations that meet with the same approval may, but the Song of the Dead feat changes spells so that they "function against undead creatures but are useless against all others." It continues, saying that "[m]indless undead (those without Intelligence scores) are still immune to [the modified spell's] effect, and the [modified] spell has no effect against living creatures or constructs."

Thus even if you can modify for free (or less!) a spell with dozens of metamagic feats, as long as the Song of the Dead feat is modifying the spell you'll just be a very efficient vampire killer or lich hunter… which is fine, but if that's what you wanted, you could've just played a cleric.

1 This reader supposes that the slaymate's powerful abilities might be deliberately gated behind at least tacit approval of child abuse, making slaymates pretty absolutely not a player-facing creature. We gamers can undoubtedly concoct scenarios that would legitimize and maybe even normalize a PC's slaymate buddy, but the slaymate really does strike me as a creature best used in conjunction with a plot rather than as a PC accessory.
2 The most widely debated interaction of sequential versus simultaneous metamagic is with modifying a spell using both the metamagic feats Extend Spell (PH 94) and Persistent Spell (CAr 81). Usual sides are 48 hours versus 24 hours and the spell's normal duration.