RYKOHL, I didn't see anywhere in your post where you had neglected your vehicle's maintenance, and you are right, you are having an insane amount of problems with a Toyota that is only a 2008 model with 74k miles. I respect the other folks' comments, but the problems you have described are happening way too early. For instance, on our '98 Sienna...
* I replaced the driver's side power window motor at 183,050 miles
* wheel bearing change was done at 220,794 miles
* I changed the o2 sensors at 260,810 miles when P0420 popped up, but am still running on the original CAT. Well, its heat shield fell off this summer, ....darn.
The transaxle was replaced under warranty at 67,055 miles due to pinion gear failure, but the vehicle now has 277,700 miles which means the trans has 210,645 miles on it, and it shifts like factory-new. It is church-mouse quiet and does not whine. I've changed the ATF on average every 24,421 miles.
Water pump is factory OEM. I may change it as a PM when the next timing belt change is due at 317,000 miles. Coolant has been changed on average every 31,734 miles.
I heard you loud and clear when you said, "NONE of these issues should be present regardless of maintenance, which I do religiously". I couldn't remain silent after it was suggested these problems are due to your neglect. You are indeed experiencing an unacceptable amount of problems with a Toyota.