The shmup stick is now fully complete. I replaced the buttons with Sanwa OBSF's w/ clear plungers, converted it to a 6-button layout, and added a new flame ball-top!
I returned my fighting game stick to the stock overlay, and ended up cutting a new port panel (by hand) out of Black Acrylic. This was done using only a Scoring Tool for cutting the Acrylic, a Rotary Tool for the rough-cuts, and a set of Shaping Files to get the clean edges and rounded corners.
Made for a much cleaner outcome this time, and used a smaller more square-sized RJ45 port (squares a lot easier to cut out evenly than ellipses):
Here's a comparison of the old Port Panel, to the new one. Definitely an improvement:
Cleaned up the wiring, added silent switches to the Sanwa JLF Joystick and Silent Pads to the buttons.
*Bonus pic: Decided to hook up my Dreamcast for some Under Defeat shmup action! My Gradius stick works really great with that game, having an octo-gate LS-58 joystick, and Dreamcast support using the PS360+ via an RJ-45-to-DC cable.