The Shield Guardian is easier to understand if one doesn't go looking for details that aren't there, and if one notes that it's not a mindless construct. Treat it like a normal creature, with only the alterations made explicit in its description, and a lot of creature defaults will answer these points.

1. Commanding the Shield Guardian doesn't require a bonus action, because it doesn't say it does. To command the Shield Guardian requires nothing other than simply commanding it in the everyday sense of the word: saying words to tell it what to do. (Note in particular that its languages entry is “understands commands given in any language but can't speak”.)

   It may be tempting to look at the Ranger's rules for commanding their animal companion, or similar examples where explicit actions are required: this is a trap, because the Guardian doesn't have any such wording. The actual normal case to compare this to is when monster A shouts commands to monster B, which doesn't have the limit of requiring a kind of action to do – they just do it whenever.

2. It doesn't say it can only act as commanded, and it does say that it has a focus on protecting the its master. It also has an Int of 7, so it's capable of simple reasoning at least, and probably more (7 isn't that far below average). Being unable to act unless commanded would be the unusual case that would need explicit statements, so default to normal creature handling: it does stuff on its own, following its own motivations (i.e., its single-minded focus on being a bodyguard), and also follows commands it hears from its master.

3. It acts on its own initiative count, because nothing indicates special handling regarding initiative. It has the capacity to make its own decisions (within its very narrow motives) absent commands, so it's not reliant on the amulet wearer's commands.

4. It doesn't say the stored spell is cast by the Guardian with “the same parameters”, it says “with any parameters set by the original caster”. Setting parameters is not required, then, it's at the original caster's discretion. This gives the original caster some optional extra control over the spell. The rest of the spell's parameters are up to the Shield Guardian when it casts it using normal casting procedures.

5. Commanding is done via words, not a special action that defines how the timing works. Words can be spoken during the amulet wearer's turn (or if your group has loosened the “on your turn” restriction, at any time), so the amulet wearer can issue commands any time they're able to speak. Either way, the Guardian will take action to follow its commands only when it takes its turn, as normal, since no extra wording indicates any deviation from the norm.

6. The Guardian isn't given a Bonus action or a Reaction by the Spell Storing trait, so it doesn't have one to use for this. It just does it as soon as it can, like any other order it follows or action it chooses itself. (It could use a Ready action to set up a Reaction with which to cast the spell, but that would just make it take longer to act after the situation arises, so it won't do that unless the situation is unusual in that the Guardian would get some warning and time to prepare.)

So far as I can tell, to summarize, the house rules change two things about item creation:

• An item creation feat's prerequisite is not caster level but, instead, effective character level equal to the feat's caster level. For instance, the feat Brew Potion has a prerequisite not of caster level 3 but of ECL 3.
• Spells that are prerequisites for creating a magic item need not be supplied every day of a magic item's creation, but, instead, only once and at the end of the magic item's creation. For example, a creature that wants to brew a potion of haste [trans] (PH 239) (3rd-level spell at caster level 20) (3,000 gp; 0.1 lbs.) need not supply the haste spell three times (once per day for each day necessary to create the potion) but, instead, only once.

I don't think these house rules will have much impact on the PCs. That's because my experience has been that players find the idea of magic item creation exciting but, in actual play, find the process uninteresting and inconvenient. It's interesting to quest for unusual raw materials or to secure obscure spells that will be used in item creation—those're adventures!—, but sitting around waiting for the metaphorical pot to boil is boring. Likewise, it's more convenient to buy magic items—price be damned!—because creating the magic item from scratch expends more of the PCs' resources than just buying the magic item outright (e.g. money versus feats, raw materials (i.e. "Still half the money!"), time, and spells—if that last is even a significant concern; see below).

Consider the dedicated wright

The only workaround I've seen PCs employ that encouraged item creation is a PC using a dedicated wright (Eberron Campaign Setting 285) because then item creation didn't slow down the PCs! And consensus seems to be that when a magic item is created by a dedicated wright, the second bulleted house rule already applies—except that the prerequisite spells are cast at the process's start rather than at the process's completion. (See here.)

War Story

In one campaign a PC had many item creation feats, but the PCs consistently put themselves on too tight of a clock to ruthlessly exploit the item creator's item creation abilities. It wasn't until the PCs were levels 19 and 20—the campaign nearing its end—that the item creator had time enough to do awesome stuff. Even then, though, it was easier to purchase, for example, several attuned gems of wish [univ] (PH 302-3) (9th-level spell at caster level 17) (33,100 gp; 0 lbs.) from the City of Brass than it was to wait over a month for the craftsman—or his wright—to make one.

So for the 2,100 gp price of a dedicated wright—assuming the DM allows a creature that participates in its creation to be considered the dedicated wright's owner (not a big assumption; Pathfinder, for instance, describes how noncasters get homunculi)—, a creature can essentially take itself off the item creation clock and put his servant on it instead so that item creation occurs, essentially, in the background, off-screen not on-screen. Further, the item's real creator need only cast the magic item's prerequisite spells once. (In the War Story campaign, the PCs outfitted an enveloping pit (Magic Item Compendium 159) (3,600 gp; 0 lbs.)—one of the game's best deals—with a laboratory suitable for item creation and carried the pit with them, dedicated wright slaving away within, creating magic items whilst they adventured.)

That 2,100 gp is a sum small enough that I could imagine just awarding the effects of a dedicated wright to all PCs at levels 7 or 8 even in an otherwise normal campaign—like a house rule saying that a caster that possesses the appropriate item creation feat and that casts each prerequisite spell once on a pile of appropriate raw materials eventually (i.e. when the appropriate normal amount of time for item creation has passed) causes the raw materials simply to transform into the desired magic item, but a caster can only have one magic item in progress at a time. I don't foresee this Easy-Bake magic item process significantly harming the campaign: the pieces are already there. Making this house rule available to everyone at level 1 is more significant, but wizards already win D&D, so it's not a big deal if wizards win a little harder while everybody else gets a leg up, too.

"Item creation feats for some, miniature American flags for others!"

I'm not sure opening up the item creation feats to any creature is the best choice. It's been my experience that those creatures that don't have access to item creation feats are already the most feat-starved. While a rogue would love to, for example, craft his own wondrous items, he's barely doing traditional rogue stuff with his tiny number of precious feats! I suspect you'll find opening up item creation feats to noncasters means there may be one extra item creation feat in a traditional party of four, and I suspect the item creation feat may be one you didn't expect, like a barbarian taking Tattoo Magic (Races of Faerûn 170) so that he can make inexpensive magic items he can activate while he's raging, or a rogue taking Craft Drilbu (The Mind's Eye Web column "The Crystalsinger (Prestiege [sic] Class)") so as to push the limits of magic–psionic transparency. In short, this, too, is not a big deal… on an individual scale.

On the campaign scale, however… wow. Remember: commoners get feats. A level 1 human commoner can now take the feat Scribe Scroll (PH 99-100)—the universe yawns—, but then that same level 1 human commoner can take any one of the feats Exceptional, Extraordinary, or Legendary Artisan (ECS 52, 53, and 56, respectively) to significantly reduce the time, price, or XP cost of magic items he helps to create! Suddenly, those level 1 human commoners are extremely popular with all the folks who can actually make magic items! Such a campaign should see magic item prices in general drop by 25% and, I suppose, an overall rise in the standard of living for pretty much everyone. And that's just to start. Like I said, this isn't particularly important to the PCs, but to maintain the setting's verisimilitude the setting must accommodate this increased access to item creation feats… especially those that don't, per se, actually create items!

With all this in mind, I'm not sure your house rules accomplish your goals. I've already mentioned how this change likely should make magic items in general less expensive. Further, the game already allows the DM to change or nix—out of hand, for whatever reason—magic items, spells, or anything else the DM doesn't like, but the house rules loosen the DM's otherwise iron grip. That is, while it normally takes a number of scrolls equal to each 1,000 gp of the item's base price to make a spell completion or spell trigger magic item, instead that one scroll can make of that spell a wand, scepter (Lost Empires of Faerûn 8), staff, or even eternal wand (Magic Item Compendium 159-60) or minor schema (Magic of Eberron 47), turning that one scroll into fifty or nigh-infinite copies of that spell! That spell the DM only put one scroll of in the campaign? Once it's found, it'll be out in the wild in short order, its DRM totally hacked. A campaign like this should have tens of thousands of crazy, niche spells because spell knowledge can spread so fast. That sounds fun and fascinating to me, but I'm not sure that's what you're looking for. (But for comparison also see the obscure 6th-level Sor/Wiz spell the Hamagess' staffsprout [trans] (Mintiper’s Chapbook Web column "Part 10: Chronicler’s Compedium").)

Finally, if a goal is to make crafting magical items accessible to any class (though not necessarily any build), that's goal's achieved, but making something accessible doesn't necessarily make something desirable—a fighter will still likely find his feats better spent on fighting and a rogue's on… doing rogue stuff. They need those feats doing what those feat already do to do what those characters need to do! To really test the long-term impact of this—which I haven't done—, a house rule would need to be made that says something like for every three, five, seven, ten or whatever levels a creature takes in classes that don't cast spells—maybe even including the first—the creature gains a bonus item creation feat. Then see what folks pick and how that changes the campaign.

An aside: nuking item creation feats altogether

When I first read the question, I thought the house rules also eliminated item creation feats—a fairly radical change but one not without precedent. That is, the Forgotten Realms supplement Silver Marches includes a magic college, the Conclave of Silverymoon (62-3), where a creature that attends can supply the cash, spells, and XP but a hapless undergrad the item creation feat. The cost for this service? Ten percent of the magic item's price. (I should note that to receive this benefit—and several others—a wizard pays per year 500 gp plus 500 gp per wizard level above 1 up to a maximum of 4,000 gp for a creature with 7 levels of wizard—a pricing scheme complicated enough to rival actual college. While this may sound like a lot of cash, amortizing this over a year to 77 gp a week should make it affordable in all but the most parsimonious of adventurers.) In other words, completely eliminating item creation feats and increasing magic item prices by 10% (plus, perhaps, a consummate increase in the cost of living?) is another possibility to consider, although such a change—unsurprisingly since it comes out of the Realms—hurts noncasters much more than it helps casters.