Runs Rough In Gear At Stop..great In Park..

Ok..replaced head gasket, new coolant fluid with Bar's leak stop to be safe, fresh oil change, new plugs and wires, car runs well but when its at a stop light is shakes..sometimes a little, sometimes alot..but put in park and it idles fine. I have no check engine lights..what could it be? I did a forum search but the problem people had was bad idle in park..mines the opisit. Any ideas? Also..replaced the thermostat while i was at it..but when I start the car the fans kick on almost right away (and its 40 degrees outside) and kick on alot when im driving..but my engine guage shows just fine. Anyone? Thanks in advance!