3.1L needs some help.....

The car - 1989 Cavalier Z24 originally 2.8L automatic , changed to 3.1L from an olds cutlass supreme but original tranny from 2.8L. Runs very rough!!!! Changed plugs, wires, air filter, new exaust no catalic converters to be plugged. The muffler used did not have an arrow, does this mean its reversible??? When mechanic hooked it up to the puter he said it was missfiring on 2 cylinders - to change the wires and fuel filter. Here it gets a little odd...... changed the 3.1L throttlebody to the 2.8L and it seemed to run good - BUT WOULD NOT SHIFT TILL 5000RPM. Was told this was the kickdown lever but I thought the same thing and unhooked it and still the same. Changed back to the 3.1L throttle body and shifting is normal. Had to unplug the lockdown torque converter because it ran very poorly and after a long drive would quit when coming to a stop. No trouble codes. Changed Idle control because it seemed as though the spring was staying completly compressed. Nothing...... same problem. Now and again it seems to work better but before long missing again. Mechanic said before 96 or 97 the ECM would not tell what was making the engine missfire. The odd thing is I drove the olds with this same 3.1 in it and it ran good but with the check engine light on. Since the change the check engine light is off until I noticed the fan ran all the time then the light did come on and told me to change the coolant temp sensor from the code given. Which put the light out when changed and now no trouble codes like I may have said. Any help would be greatly appreciated! Now that its always running like this instead of sometimes could this be faulty coils and how would I find out if they are or not???

Trevor