...this class is making you a worse wizard *and* a worse artificer, all at the same time...
This is true of all theurge PrCs I know of, fact is you're doing both at the same time. As it is now, you can get to effective level 15 in, let's say Wizard, by level 16, dropping 1 single paltry level of spells for the sake of also counting as a level 11 Artificer for infusions/day (but at level 15 CL).

This is frankly ridiculous in my mind, you're talking about a near-gestalt build PrC. It's now so far off-balance that the scales have been lost completely.

If the balancing were up to me, I'd be far more tempted to drop spell/infusion gain COMPLETELY at levels 1 & 10, since this class is looking a bit pokey just now. At least that way, our Wiz 5 / Art 1 / Artytheurge 10 would only count as a level 13 Wizard, level 9 Artificer (at CL 13), with a couple of really nice abilities to augment his buff potential.

This is before I even get to the fact that a Cleric could come through this the same way, and with the buff/debuff potentials of that mix, these guys could break encounters.

With that all out of the way (sorry about the rant), perhaps it's time to address wording issues!

Infusing the Arcana needs expanding. After it says;
...you may use any Infusion that you know
you should add:
'with an infusing time equal to or less than the casting time of the spell. This requires no additional time, the infusion is used as part of the same action as casting the spell, upon the same target as the spell. If the spell could target more than 1 ally (yourself included) then the infusion applies only to the first person touched.'

I think that covers most eventualities!

Artificer Abilities should probably drop this line:
The bonus feats gained this way or through Artificer levels from now on also allow you to choose wizard bonus feats.
It's a nice idea, but with the 'feat swap' caveat you threw in a couple of days ago, the above line becomes a completely moot point.

Familiar Homunculus could be simplified by removing the second line and putting in it's place 'Refer to table on page 53 PHB for these bonuses.'
Also, this ability is only any use to arcane (and not even all of them) casters, any other class won't get the benefit. I doubt it's a problem, but I feel a bit sad

That's about it for now!