OK, so it's finally in, but not without a lot of grinding, filing, and test fitting. The inside curved part of the flange needed to be thinned out quite a bit. It was mis-aligning the pump and causing a gap between the pump seal and the shoe. If I laid the shoe on it's back (pump mount side down), the inside of the shoe flange was not the same thickness all the way round and pretty rough to say the least. It took me over two hours of grinding and filing to get the thickness right where it mounted cleanly, especially the curved part near the top of the pump tunnel. And once this was done, my original holes lined up perfectly.
I think this was a great part, but with a little more attention to detail, it could absolutely be a drop in item. Hopefully I never have to do this again.