The bootleg is such a close copy I was able to run the top board with a bootleg bottom board and vice versa. The main issue turned out to be a 'slightly' faulty Z80. I've never seen anything like this, it passes in my chip tester and works on most other boards, ZX Spectrum etc but putting it back in Gemini Wing it refused to run.
With a new cpu in place it ran but with missing player / enemy sprites and no sound. The sound issue was due to a missing M5205 (quite hard to find these days, also used on Double Dragon). With this replaced the sound returned and just left the sprite issue.
I found two LS257s on the bottom board with floating inputs, I traced this back using the bootleg board to a LS193. 193s aren't something I've ever needed before so didn't have any stocked but luckily I found one on a scrap board.
With the new 193 in place the missing sprites returned.