First task was pump alignment.
The inserts were all straight and square to each other. The pump bolted in fine. When I added the OEM shoe the alignment was off left to right and front to back. I was off by about 3/16.
I removed all the paint from the shoe area and it was closer. I continued to grind down the fiberglass and plastic shoe till they aligned properly.
I also had to add 3 washers to the top and 2 to the bottom to get proper compression against the seal. Without any shims the shoe would just slide out.
After all the alignment issues with the shoe I thought for sure the midshaft was going to be off. But to my suprise it was perfectly centered left to right and the cold-fusion tool helped by quickly identifying the shims I needed on the back of the pump.