The only issue I realized is, that the top cover might be thicker as needed.
Aluminum isn't as strong as the original thinner steel plate, especially considering there is now a large hole in it, so opted for a thicker material just to be on the safe side. Anyone is free to adjust this thickness as well as the panel color in the FPD application, but no guarantees that a thinner material works out better. So with the thicker panel you get a ring of silver colored aluminum exposed around the top edge, which still looks good in my opinion. Good to hear it fits.
On that cart tunnel fit issue you mentioned, do you think it could relate to the cart connector being off center when it got soldered to the motherboard? If not, let me know if you think it's an issue requiring adjustment, since I could always nudge the hole in either the X or Y direction if needed. This stuff is hard to get perfect on the first or even second go around, due to the difficulty in taking measurements when things are not all on the same plane.
BTW, I use 6-32 x 3/8" flat head screws to secure the cart tunnel to the board (the screws will self thread into the PCB for perfectly aligned fit). I then twist on some .25" x .25" 6-32 threaded round aluminum spacers underneath which serve as supports to keep the board from bending when inserting carts. I should probably post a pic.
You'll need to glue in that rear panel when you get the CF adapter mounted, since pushing in that CF will probably loosen the panel over time.