Car runs much better now. HOWEVER, still idles up/down,

Vacuum/intake leak it sounds like.

I have the same car, tranny, engine you do.
Mine idles up and down between 500-700 at idle with the A/C on, otherwise it doesnt. The idle is slighty rough, but I have done many of the things you did already and it fixed to the point where I'm happy with it.
I was told by a shop they cant figure out why the idle goes and down only with A/C on.

I would check your vacuum lines for cracks, and replace your intake gasket.