I gut the centers out of the thermostat. Leaving it out altogether is not good - you want that point to be the bottleneck to keep pressure in the block higher so don't form steam pockets.
But gutting the center out, buys you time for breakin, flows the most water, runs the coolest. During breakin that is the ideal setup.
Hard to figure it running rougher hotter if the choke was off the whole time. Sometimes on warmup the hot exhaust iron will push the whole manifold away from the head, creating an intake leak. But usually not with an iron intake.
