A quick test fit and it looked much better. With the excuse of better clearance as well as to vent some frustration I beat the crap out of it with a BFH (big fancy hammer) clearance even better.
I bolted it up temporarily and decided to bolt up the master cylinder as well and had a moment of panic when it hit the power steering pump. Then I remembered that I had removed the belt and had the pump in the full upright position when I was flushing the system. As soon as I put the pump back in its normal position the master cleared just fine!
With that imagined crisis over I started making a template out of cardboard to A) make sure there was room to slide a cover over the hole and B) to get an idea of the shape I would need to cut out. Here is what I came up with:
Another whole day killed, time to go out hunting again...
-Richard