Same here, I needed to do this on my foot rocket. I flipped the stator section and clearance for everything was much better. However, I think you should make an attempt to align your pump since the dowel pins had to be removed. I just took two 1x4" pieces of wood (set on a flat surface) and set the pump on it while tightening the long pump bolts. Make sure all four bolt locations touch the 1x4". I can't figure out how to explain it very well, but you basically don't want to have the pump twisted when you bolt it in. The same shims could have completely different results on a twisted pump vs a pump that was square when the long pump bolts were tightened.
Hope this makes sense.