Compared to a traditional r/c the u looks a little out of place, but for a custom build I love it!
There is plenty of strength there, a few random holes won't weaken anything, I say you cut holes to run wires and further cleanup the wiring. I like what you did with the motor wires.
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It's "Dr. _paralyzed_" actually. Not like with a PhD, but Doctor like in Dr. Pepper.