Note: This answer is primarily from a 3.5e perspective. Changing this to a 3e perspective doesn't change much so far as I'm aware.

It's not as good a deal as it seems

Bobbi the Builder, a level 13 wizard who possesses the feats Craft Wondrous Item (Player's Handbook 92–3) and Craft Magic Arms and Armor (PH 92), labors for a month in a 500-gp laboratory. During that time, she also succeeds on her Craft (armorsmithing) skill check (DC 20) to sculpt from 500 lbs. of pure iron a magical iron golem limb (Monster Manual II 209). To finish the rituals needed for the limb's creation, she spends 20,000 gp on raw materials and 400 XP, and casts the 5th-level Sor/Wiz spells cloudkill [conj] (PH 210) and 6th-level Sor/Wiz spell geas/quest [ench] (PH 234–5). She puts the limb in her Heward's handy haversack (Dungeon Master's Guide 259) (2,500 gp; 5 lbs.) in case of an emergency.

Attaching the limb

While on an adventure, there's an emergency: Abe the Unlucky reaches into a sphere of annihilation (DMG 279) (minor artifact; 0 lbs.) and, rather than "suck[ing Abe] into the void, [leaving him] gone, and utterly destroyed," the DM rules that only Abe's arm is utterly destroyed. Traumatized, Abe looks at his stump, whimpers, and collapses. (Limb loss in 3.5e is typically at the DM's discretion.)

"I've got this," says Bobbi, and she whips out the iron golem arm. (That she has an arm is enough; handedness, fortunately, isn't really an issue in 3.5e.) She takes a standard action to attach the golem limb where Abe's original limb once was. That's because

Once created, the limbs are treated as spell completion items. Any character capable of casting the appropriate level of spell (see specific descriptions) can attach a limb. [An iron golem limb requires the creature doing to the attaching to be able to cast 6th-level arcane spells, which Bobbi can.] All that’s left to do is perform the final gestures and speak the words needed to imbue the limb with magic. (MM2 209)

This is Abe's first iron golem limb and, after it's attached, his body'll never be able to accept a different kind of golem limb. When the golem limb's attached, Abe makes a Will saving throw (DC 15).

Making the saving throw

Contrary to popular belief, a creature cannot opt to fail saving throws against anything. Creatures can voluntarily fail saving throws against spells (and, by extension, spell-like and supernatural abilities, which are like spells but with exceptions) and a few other similar cases (like psionics) and edge cases (like drugs), but the Will saving throw mandated by the golem limb is neither spell, similar case, nor edge case, so Abe can't opt to fail. (A creature can have effects applied to it to reduce its chance of success on a saving throw, but a 20 will still succeed… except in 3e, where a natural 20 on a saving throw isn't an automatic success nor a natural 1 an automatic failure.)

If Abe succeeds on the Will saving throw, he's gained a pretty significant amount of power asymmetrically: he gains the half-golem template except he retains his own type and gains a +4 bonus to his Constitution score. (And, as the template includes a golem's magic immunity, he'll likely need this power unless the DM allows Abe to lower an immunity voluntarily, an act legal according to one parenthetical example abesent from the SRD on Voluntarily Giving Up a Saving Throw (PH 79) yet nowhere else in entire D&D 3.5e corpus.)

If Abe fails the Will saving throw, the text makes it sound like Abe should become an NPC. That's because failing the saving throw means Abe

becomes a half-golem of neutral evil alignment. The character then has no Constitution score and the character’s type changes to construct, granting him or her construct traits. A neutral evil half-golem retains the memories and knowledge of its former life, but its personality becomes murderous and cruel. It demonstrates [a] hatred of flesh creatures… and it seeks methods appropriate to its class to slaughter as many flesh creatures as possible. (MM2 209–10)

Nonetheless, a DM could still let a player continue playing such a character in an atypical adventuring party. However, the Monster Manual II on Effective Character Level, in part, says

Some of the creatures in this book are capable of having levels in a class, and when they do, they are significantly more powerful than the races described in the Player’s Handbook. This difference in power is expressed as the creature’s level adjustment (a positive number). This number and the creature’s Hit Dice are added to the creature’s class level to determine its effective character level, or ECL. (21)

And, while some creatures in the Monster Manual II do have an ECL, the template half-golem has no general ECL entry, and the sample half-golems—all of them constructs that, apparently, failed the golem limb attachment Will saving throw—from the Monster Manual II (209–12) and its Web enhancement "More Half-golems!" (1–5) don't have an ECL either. They just don't appear to be appropriate for PCs, despite their Advancement entries. (The D&D v.3.5 Accessory Update lists the LA of the Monster Manual II's printed half-golem templates as LA —, and "creatures suitable for use as player characters or as cohort" have an entry that's not LA — according to the Monster Manual (7) for 3.5e. So in 3.5e such creatures really aren't appropriate for PCs.)

Incarnating afterward

Thus this DM assumes that slapping a golem limb on a dude is legit, and the creature, if a PC, remains playable. The downside of magic immunity (if it can't be lowered and, perhaps, even if it can) is such a significant impairment that getting a metric crapton of bonuses is necessary for the PC to continue adventuring at all, and, even then, probably not for long once the novelty wears off. Note that this PC is an ineligible target for the 9th-level Sor/Wiz spell incarnate construct [trans] (Savage Species 67–8).

However, this DM can't imagine a creature that wants "to slaughter as many flesh creatures as possible" agreeing to fail the saving throw against the spell incarnate construct. Okay, this DM can contrive a scenario where that might be a thing ("By taking on a fleshy form, I shall be able to fit in better among the fleshy and slay more of the fleshy! Muhaha!"), but the half-golem's magic immunity (if it can't be lowered) will negate the spell incarnate construct anyway. Yet the existence of the incarnate stone golem (SS 120–1) means someone found a way to cast the spell on that stone golem, so maybe this half-golem could find that caster…

But that's really complicated. In short, a PC could get a golem limb, fail the Will saving throw, and become an NPC. Then that NPC could find a creature who can cast the spell incarnate construct in such a way as to bypass the NPC's magic immunity and become eligible for PC status once more, but the DM must determine that PC's ECL. This DM suggests that this ECL be the PC's Hit Dice −2. The template incarnate construct removes most of the PC's special abilities, including all special attacks and special qualities, which is pretty much everything previously gained from class levels.

It seems too weak.

From the DMG p. 273 onwards, if you make the math:

For defensive CR:

It is not resistant to Slashing, on the opposite, it is vulnerable. As it is resistant to Bludg. and Piercing, I would say it doesn't change the CR, but by strict DMG ruling it probably would have even lower effective HP. With the HP you got there, it would be a CR 1/4 monster. As the AC is only 1 point above the usual 13 for a CR 1/4, it stays at CR 1/4.

For offensive CR:

The Pack Tactics means +1 Bonus on attack. The Pounce increases the DPR by 1 for Claw, which is still lower than the (effective) 11 from Bite (due to the prone effect, +1), so that is our DPR. That's a CR1 monster. A CR1 monster would have +3 Bonus on attack, but your Wolf has +5, so it becomes CR2.

Final Rating:

\$ \frac{1}{2} \left(2 + \frac{1}{4}\right) = 1.125 \$

The DMG says that you should round it up, but honestly it seems just way too weak even for a CR2 monster. Honestly, this seems a CR1 creature, but since it is so unbalanced between Defense and Ofense, you shouldn't put it against a Level 1 party, as it could potentially kill their Wizard. Still, it's clearly weaker than an Ogre, for example.

Your questions at the end are... lots of questions. It is too UP for a CR3, Slashing Damage is a vulnerability that decreases the effective HP by alot, as stated in the DMG, so no it's not good. The next questions are about balancing encounters, which is a totally different question and is answered in p. 81 from DMG or p. 56 from Dungeon Master Basic Rules.