If every motor you try is heating up, there is something in your track or transformer causing the problem, not that many motors all get hot at one time, have you taken the suspect engines to another track and tried running them to verify ?
I, like Rolland above, run long consists with grades. I seldom have a heating issue, I just upgraded a set of Lionel F-3 pullmor to Williams can motors and trucks, have both A units double motor, and run 15 aluminum passenger cars behind it for hours and they get warm but not hot. My layout is fastrack 048 and 060 with a Z4000.
The few Williams I have had get hot had an issue with the truck or pickup, one also had a bad wire to the e unit which smoked the e unit but the motors were good to go once put a bridge rectifier in for forward only.
