Have you looked at your ecu? There is a large thread about leaking capacitors causing all types of issues (low rpms, shifting issues and many many other things). My 2000 gs400 does show some of these signs, it'll hold on to 1st a little too long and the same with 4th to 5th. But only on a cold drive. I have done the drain fill drain fill and went through more than 10 quarts of t4. Although acceleration was slightly increased the other symptoms remained..... But I have yet to check out the ecu (I break everything fragile). That's my two cents. I hope you find the issue and keep us posted.

 

Checked the ATF fluid today, still clean and was the right amount necessary. Had no jerking tranny issues for the past few days. I'm curious if it could be weather related?