But that's the problem. Rich Burlew's fix makes sense, but it's a university thesis. I'm sure your rewrite is great, but 6 pages is way too much IMO. It's a spell (or four, but you get my point). 98% of the forms you'll use pose absolutely no balance issues - then there's the 2% or crazy stuff. There has GOT to be a way to fix that without requiring your players to take night classes just to navigate the convoluted exceptions and counter-exceptions of a lengthy houserule.
Changing it to make a player use the monster's stat-block wholesale instead of bizarrely stacking stuff on top of his own abilities already fixes any and all spellcasting-related balance issues. If you want to get technical, just say that the character keeps his mental scores for the purposes of, well, understanding what's going on but not for spellcasting. Or something. All that's left then to fix is abilities that are overpowered by themselves when infinitely available to PCs. There can't be all that many, and there's got to be a way of getting rid of all of them.
Finally, there's the writeup of the spells to change. I'm leaning towards merging them into one, variable-level spell: you prepare it in a level X spell slot and can pick forms up to 2*X HD or CR, whichever is the highest. The one point I'm still on the fence about is whether one spell gives you access to all forms, but you need to prepare it with a specific form un mind (which screws over Wizards and other prepared casters) of if each form should count as its own spell (which screws over Sorcerers).