These things are normally very reliable, but I've got a few problems.  It's an SR5 3.4ltr 4wd Auto with a well maintained 120,000 on the odo.

Problem 1:  Twice the transmission has slipped in the forward gears when it AND the environment are cold.  It tached up to 2,000-2,500 before it would start to move and then only barely.  It's in the shop right now for this one, and they've yet to replicate the problem, but it will be cold tonight so we'll see.  When it was slipping I tried all forward gears to see if it was a selector problem, but it behaved the same in all gears.  Reverse seemd to be unaffected, but I can't tell if was do to proper function, or just a much lower ratio making the tranny work much less hard.  Hydraulic problem or worn forward gear clutch pack?  DOAH$$$$$

Problem 2:  I'm getting a serious miss, as well as what seems to be a backfire into the intake when the engine is cold.  Power is lost, and muffled random popping is heard from the engine.  This is NOT ocuring under idle, but starts under even a light load.  It's bad when first started, but slows down, then goes away once warm.

Comments?  

I hope by "the shop" you mean that you took it to a factory-trained Toyota technician.  The scabby corner transmission shop probably isn't going to be able to help you with this one.

You will need to be able to demonstrate the transmission concern for the technician before he will be able to properly diagnose it for you- imagine going to the doctor and telling him that your stomach hurt yesterday, and expecting him to tell you what's wrong with you.  Intermittent concerns can be like that.

As far as the engine miss, you'll need to take it to a factory-trained Toyota technician.  Should'nt be any problem at all for him to diagnose this one for you, since it sounds like it does it every time.

has the tranny filter and fluid ever been changed?
+2 on taking it to a dealer.
they'll know better amd have the right parts to fix it. not all replacement parts are created equal.....
too much [omputer crap on that one to be interguessing on it.