ChicagoRuss19

I drive a '96 2.5TL. Recently I replaced that engine (180,000) with an engine off a '97 2.5TL (90,000). I replaced the throttle body, air duct, alternator, belts, water pump, timing belt, and all seals. I did a fuel induction system (3-step) I cleaned the EGR chamber and EGR valve with cleaner. Finally I am about to replace the wires (NGK), plugs (Iridium), distibutor cap/rotor (with two gaskets) and air filter (K&N).
My vehicle hasn't been passing smog, but i'm going to check it after I replace my parts. HOWEVER, one thing I have noticed is that my engine heats up a lot (to the point where you can smell/feel it while driving). Do you think this could be because of the thermo sensor (the one connected to the thermostat). Could this play a factor in why: I'm not passing smog, my vehicle's engine heats up (even though the fans are functioning), and decrease in power?

Answers would be appreciated!