[Bill Bess]

HMMMM! Check to see if all your hoses are okay and not caving in while under pressure, burp the system, and veriy the heat problem with a temp. gun. Your gauge cold be going south so verify the gauge is correct.
When does it heat up? at idle, at speed, during acceration, fan on fan off, does it stay cool without the fan while crusing down the road at 50mph?
Could be a comb of things...what did it run at prior to the rebuild?, what's different now?
Could be a combination of issues, larger bore, fan not cutting it while under way (low amps. to fan). Maybe try to back flushing the system to verify tha no obstruction exist. Just make a list and check them off as you verify each potential cause. You might consider a Ford Taurus fan to up grade what you have (two speed), this fan has helped many cobra folks including me.
Good Luck, Bill