I just re-read the original post, where it said that it had a water pump and fan clutch from a 60 - which would mean a couple things. 60s have an oil cooler and an extra hose fitting for the oil cooler. What happened to that? Is it blocked or do you have an oil cooler (with corresponding t-stat housing with hose fitting)?
And, fan clutches are notorious for not working properly. Even new ones. Mark Whatley has written about how all the aftermarket fan clutches he's been getting lately are too small to be effective for a 2F and he's gone back to OEM. Used ones can have worn out silicone fluid or none from leaking out. They can be rebuilt and new fluid is available from dealer. I've seen more stories about overheating problems solved by replacing/rebuilding/replenishing the fluid in the fan clutch solved overheating problems in a stock setup than any other cause.