So, did you just jack up the back of the assembly by raising the cross member? I'm sort of surprised that this is causing a problem for the rear output. I've raised mine, but not quite that far yet, and had no issues. But I had planned on going higher still as soon as I ditch the engine mounted fan (which already hits the trimmed fan shroud).
I guess I would be tempted to just try to estimate where the desired level should be and figure out a way to get it there. Drill and tap is a possibility if you have it coming out anyway, but I hate pulling that thing. So, I would probably just rig a "L" shaped filler in the stock hole so that I could poor in from the top to get it to the level I needed. Next time out, look into redrilling maybe. Hmmm, might even be an opportunity to build in a sort of sight glass for quick visual checks of fluid levels. Just shooting from the hip…
I'm interested to see what comes of this post. Good luck...