I'd bet that you forgot to bleed the coolant system for air bubbles. They get caught behind the T-stat and freak out the temp sensor. It causes the ECU to freak out and makes the engine run like crap at low RPMs.

Another thing to check is the timing of the engine. Sometimes higher rpms can mask misaligned timing.

Erik P.
Official 2GNT thread Hijacker
Some say that he's driven over more Covenant than he's shot, and that his grenades aren't where you'd expect them to be...
All we know is, He's not The Stig... But he is The Stig's Spartan cousin!