I am no expert, and have the 22re/auto, mine shakes when I put it into D or R and I am guessing it is a vacuum leak. I replaced my EGR, cleaned up the intake flap, replaced the PCV valve and grommet, adjusted the timing, replaced the distributor cap, and wires, and got a major improvement in the idle. Mine was so bad that my foot would hurt.

I suspect there are still vacuum problems though bscause the aftermarket cruise I put in doesnt have enough pull to shift the tranny and it loses lots of speed up hill.

Because I saw improvements in fixing some of the vacuum problems, I am still chasing that idea.

My other theories on this:
Torque converter is getting old, although I took it to a tranny shop and the guy put his foot on the brake and gassed it in drive and reverse and said the torque converter is fine. beats me as to what he was doing.)
2. Harmonic balancer is bad (I don't know what this is exactly, but usually something vibrates when it is out of balance, so its a theory.)
3. Tranny mount is bad. The engine is vibrating but I can't feel it in neutral or park because the vibrations are not transfered to the frame.
4.I need to do a valve adjustment. Timing is good, but if valves are off, could I be getting vibrations?

As you can tell I have given this some thought, but not being an expert, my thoughts may be wacko.

I wanna hear other suggestions, hopefully EB will chime in, I am guessing he would know.
I have also heard of Toyota engines having this in common, even when new.