Problems

Hey I got a question for you guys.
I have an 89 lx N/A. A couple of years ago the transmission went out on it and I had to take it out to get it rebuilt. I just got the transmission and car back two weeks ago and the thing runs like s***. When it starts to warm up a little bit it does not idle, it will start dieing. It got a tune up before the transmission went out so its got new plugs, wires, cap, rotor, battery, alternator, radiator and a thermostat. So I know it is not plugs or anything. I put iso-heet in the tank and then filled it up with premium to try to see if it was just water but half a tank later it still does not idle at all. What would you guys suggest to fix this or where should I start?
I also just realized that there must be a cooling problem as well. The fan does not work any more and when you squeeze the upper radiator hose you do not feel anything moving through the hose. Do you thing the thermostat needs to be replaced again? Also what would you guys recommend for the fan issues?

If anyone could give me feedback that would be very appreciated!
Thanks Everyone!
Alex

I checked the timing and it seemed fine it was right on @10 degrees. I checked that right away because when you first go to give it gas it would sputter then kick down??

Yup...it was out. Anyone got any other ideas? I am changing the thermostat now just to be on the safe side either way.