So as it is currently, there is still gelcoat on the aft face of the hull where the shoe will get glued to. I wanted to wait untill I have the final location of the shoe set before I removed it in that area. Sides of the tunnel are all clean. Now I realize the gelcoat does have some thickness to it, but not much. With all of that said I have tried bolting up the pump with the seal on it and I physically cant compress the seal enough on my own to get the fwd bolts in without crossthreading them. I could probably do it with 2 people if I had to but I would rather avoid making that a necessity. I also never had this issue on my SJ and this is going to be my best opportunity to correct it. As for how I would adjust that dimension it would either be by removing material from the shoe, the hull or like you said elongating the holes some.
So currently I have 0.075" +/- 0.015" all the way around between the front lip of the wear ring, without the seal on and the shoe. And to address Big Kauhuns comment, that is with the shoe shimed square to the pump with washers.
I bring all of this up because I helped my buddy align his pump on his maybe 4 year old edge last month and his gap was so small it was almost impossible to get his pump in. At one point we even tried ratchet straps. Lol And to make matters worse his inserts were almost totally destroyed from being cross threaded in the past because of how tight the pump was. I'm just trying to avoid running into the same situation.