The shaking after hot is a typical problem.
These are the things that I had to do to tame my shaking in the order of what helped the most:
Rebuilding the Injectors; new Spray Nozzles Balanced and Tested (by me) took out the bulk of the shaking. Looked like at 198,000 miles I had the origional Injectors in the Engine when I bought the car.
Next best was doing the Valve Adjustment
Replacing the Motor and Transmission Mounts
Found I had a small air leak due to Fuel Inlet Hoses too hard to tighten. Only leaked air when Engine compartment was warm.
Fine tuning with the New Rack Damper Screw (it did not have much effect until I did the above list of things). No turbo= no Rack Damper Screw on your Fuel Injection Pump.
If you do not believe you have an Injector issue and all that other stuff
The Vacuum Leak might be effecting your transmission or it could just be wear.
Here is the other stuff on tramissions:
http://www.continentalimports.com/ser_ic20242.html AUTOMATIC TRANSMISSION ADJUSTMENT ARTICLE
WIKI Transmission adjustment
http://www.peachparts.com/Wikka/TransVacTune
Transmission adjustment Thread
http://www.peachparts.com/shopforum/showthread.php?t=158216