Tell us more about the tranny shudder. You said comes and goes. Does it never get worse over time? Have you ever had the transmission serviced?
Like I mentioned, it's been there almost since day one.
The shudder is very minimal but does come and go in waves.
The first wave of "getting bad" (which is still minimal) my wife and I were in the middle of moving so we had too much on the go to worry about it and since it was so minimal I didn't worry much.
Then it sort of went away for a while....
The next time it started up again I had about 50,000km on the truck and decided to change the fluid. I have been changing the fluid ever since then every 50,000km or so. The problem does not seem to be affected by fluid changes, or pulling a trailer or weather etc. and hasn't really gotten any worse (or better). I've seen way too many horror stories of auto trannies being ripped apart and never being the same. Since it doesn't really bug us or or seem to have ill effect, I've just left it. I did a little reading and found one generation of Lexus (I can't recall the model now) that had a similar symptoms. Toyota did a firmware upgrade on the lexus as there was a bug that caused the tranny to hunt between gears when up-shifting. I have it in my head that our tranny is doing the same thing. When it starts to do it, if I change the accelerator position slightly (either way) the tranny shudder settles down. When it's in it's mood, the shudder is worst when shifting from 1st to 2nd and less noticable when shifting between 2nd and 3rd and doesn't seem to affect the next up shifts from there. Never happens on downshift.
As mentioned, I change the fluid every 50,000 km, use only the toyota recommended fluid (WS) and follow the toyota proceedure to a tee.
I have read numerous posts on people having shudder issues with these trucks that required new torque convertors and trannies, I really don't want to go down that road unless it got worse.
It does seem like there may be an issue that Toyota can't put their finger on though....not sure.....

At this point, we have more than 1/4 million kms on it and the tranny has never failed so perhaps the issue (what ever it may be) might be more of a nuisance than a real problem!?
I've worked on machines long enough to know, if it's not really causing you trouble, don't bother, otheriwse it usually opens a can of worms!

Hope that helps!