alright, this is what i would do.
first, when you put your LIM (lower intake manifold i assume is what that stands for?) on you should have cleaned out the bolt holes throughly. if you didn't there could be some thread lock in there, or you could have some RTV in there from when you put your gasket on. thats a suggestion as to why the bolts will not tighten to spec. a good rule of thumb on bolts where torque settings are important is to just replace the them. it just knocks out a potential variable.
second, as far as you radiator goes. get the car warm, and check to see if it's leaking from the radiator itself. i had a pinhole crack in my radiator that would only leak when it was driven for a long time to get hot enouogh for the metal to expand and start leaking. since my drive to work at the time was like 10 minutes, it took me forever (and a overheating) to figure it out. as far as your thermostat goes, it should be opening. try boiling it in some water with a thermometer in the water (a cooking thermometer). see what temperature it opens at. you may have a faulty thermostat.
if your car dies when when you come to a idle i would check your IAC to see if it's working. it SHOULD throw a CEL, but sometimes doesnt from what im told. of course, it could be a vacuum leak at your LIM because your bolts aren't torqued to spec.
if im not mistaken you had all the trouble getting another engine right? like a junk yard gave you a FWD, etc.... if so and you swapped in this motor, check to make sure you got the vacuum lines hooked up properly. could be just a simple oversight.
another thing that popped into my head is you should have a sensor (intake vacuum sensor i believe, someone correct me if im wrong) on the back part of the LIM (at least my 94 does). check to see if it's plugged in.
hope some of that helps, its what i could think of off the bat.