Cooling/heat issue/s :/

[mx6rrr]

I have a 90 all-trac replaced the thrmostat 3 times and just replaced the radiator and the cap (cap twice)...havent done a flush yet but the coolant was very nasty coming out of the car when I drained it from the radiator...The car used to stay at normal op temps when idling but when hit the highway speed creap up and go back down (like the thermo was stuck)...anywas I yanked the thermostat for troubleshooting and she does alot better now, less issues when its warmer out (its been really cold here in wisconisn)....
Another question while Im at this point...if the heater core is clogged will it cause temp issues with the water temp?
Im hoping is just a clog somewhere and not a head issue!
Anyway to tell other than just getting it flused and finding out that way??? Or anyone have any better ideas?? Im frustrated!
Also, just to point out...it likes to smoke out the radiator cap, i kept the cap off and ran it at idle for a bit just to get the air out and it was smoking, if I run the car around town for a bit (like I said shes doing better now with the new radiator cap and no thermostat but) she smokes a bit more but the temp is staying down...i drove it for about 10 miles she was fine, hoped on the interstate for about 3 miles and she started getting hot again, soon as I got to an idle she started coming back down....???