One idea is to make sure the fuel mixture isn't too lean. That could cause the engine to run hot. Try opening up the mixture screw and run it slightly rich and see if you get better results. Also, beware the dreaded effect of ethanol on rubber parts in the fuel system. I once put a fuel pressure regulator on my TR3 and the car ran great for a day, then the next day it wouldn't start. I removed it and let it sit, reinstalled, and same thing -- the car ran great for a day then wouldn't start. The problem was the ethanol was causing the rubber in the regulator to swell, choking off the fuel supply. I'd definitely would address the cleanliness of the cooling system as you are planning.