Well, first of all with an EFI/MPI engine, don't even THINK of running without a thermostat. The engine will be in a rich mode way too long and the combustion chambers will load-up with carbon deposits. They could start glowing and cause detonation.
I have seen removing the 'stats and the overheat stop, but you fixed the result, but not the cause...unless the thermostat itself was no good.
Check the risers for possibly being plugged and keeping the water in the engine too long, or you just may have a failing raw water pump impeller.
Don't forget the "Bravo Syndrome" as a possibility too.