Thank everyone for all of the replies! I eventually got the case smoothened out. I polished the inside of the case pretty heavily which helped a lot. I ordered dies at the same time as the modified case, but I still have yet to receive them. Therefore I was a little limited in my route to fix the issue. I'm getting pretty consistent results now. I will be using neck sized fired brass and plan to move on to calculating ogive to shoulder to make sure my distance to the lands is adjusted correctly to the brass I'll be using.
I do have a question though. It seems when I measure to the lands with my EOL and VLD i come up with a different number to the lands. In my head it should be the same distance to the lands regardless of bullet selection if the only thing I change in my testing method is the bullet. Using the same gun, comparator, and tools. Why would a get a different number.