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Looks like a cool set up as it is. You could just drill a hole through the top and print a mount for the ts with the cable going into the existing box through the top, something like this (the center part)

This is also really cool looking and may check some of the boxes:

Were you planning to use a t/s that connects with the flat cable? I was thinking of buying one of these for my printer, and it uses HDMI and USB so cable length would not be a problem (could be moved remote from the control box):

Squeeze Pi Enclosure
3D Printer Electronics Enclosure - Touch Screen, Mainboard, MOSFET, PSU, Raspberry, Fan.