It's a shame about the fitment issues. Shame those CPU and PPU interposers can't be soldered to the pins of the CPU/PPU from the underside in a similar fashion to your NES-101 reset circuit and the TG16 region mod. There's a bunch of space under the board and those CPU/PPU pins are straight. It'd help with your clearance issues and also yield a faster installation. Just an idea which I don't know how feasible it would be to implement since I don't know if those interposers just T off the pins or if they interrupt any of them. The ribbon cables could be run from under the board to the top using the shielding hole near the power switch (not sure of the ribon cables dimensions or length).
Also, I've been toying with ideas and implementation for a NES-101 rear panel design for this using those HDMI extensions mentioned in this thread previously
As far as HDMI template and routing go; the cheap way to do it might be to kluge together a hole making tool like what they use for refilling toner cartridges (it's kind of a mating of a metal hole template and a soldering iron)
://www.ebay.com/itm/like/19093470...
If you could put the metal part of an HDMI port on that tool you'd have something you could use with your template to make a much cleaner hole, quickly, and then clean it up a bit with your files if needed.