Just to update the situation, I had the fuel filter replaced and the acceleration seems to have been fixed now. The weather here is is kinda crappy, rain/wind so it's a little hard to tell but it feels better to me.
The idle is still rough when the car is warmed up. It's where it needs to be ~500-700 rpms. I believe the motor mounts are ok. I don't see a lot of movement of the engine when I rev it up. It vibrates the steering wheel and the whole car when it idles. I can see the steering wheel moving.
I read some past posts and the idea that the balancer belt could be off a little and this could be my problem. I'm the 2nd owner of this car and bought it with 125K miles, so I am assuming that the previous owner had the timing belt, etc done. The car is a 5 speed and it idles rough when it it's neutral and also when the clutch is depressed and I'm in 1st gear at a light and I am waiting to go.
Any other help would be appreciated, thanks!