Help! Do I cut it out??

Don't cut the x member. It's there for support. The 1-2 and 3-4 rods go above the x-member and the reverse rod goes under the x-member as in the pics above. I'd wait and dry fit the bell, trans, x-member, shifter, rods, and hump before you paint. Once in place, you'll know exactly where the hump should be welded in. I recently installed a 4 gear in my 69 Dart and that hole just doesn't look big enough.