The map was made entirely out of power 4 displacements, so the visual bugs are just a result of mass changing them. Reducing the power of the disps did not fix the issue however, so I had to manually find 8 or so displacements out of hundreds that were causing the game to crash, by using trial and error with the cordon tool.
If there isn't anything that changes the way the map is played, I don't think I will be updating it further. My goal was to fix the map with as little change to the jumps as possible, I can upload the vmf if you or anyone else would like to fix the visual bugs.