Regarding pan and HV oil pump fit, I have exactly the same experience, although this is with stock pan, so this info is in the "for what it is worth" category.

I ran into clearance issue, attempted to deal with it by putting some dimples in the factory pan. That pan was really thick so I thought there would be enough room, alas as it turned out maybe too thick actually to make it work.

1) factory pan with oil pump clearance dimples - early stages


2) and here is the resulting crack


..so that put an end to this idea. Well, I re-grouped ha ha...and off I went looking for alternative oil pumps to see if I could eek out a little extra clearance.

Here is what I arrived at:


...and as tiny as it may seem, the recessed screw mounting pad of the oil pump cover along with the lower profile of the bolt head actually shaved off enough to make the pan fit work. It was probably about 1/4" clearance.

Not sure if you looked at alternative pump covers, but maybe that's a viable approach to get you that extra clearance?