The board was working apart from the character layer of the graphics, making the text scrambled and blue blocks appear over the background and other sprites.
I didn't notice at first but blue and green were also switched, this was an issue with the adapter though and not the board.
The first thing I did was dump all the eproms and make sure they matched the ones in mame. Eprom 5 failed but this was a red herring as it was fine even though it's not in mame. :)
This did lead me in the right direction though as the data causing the issue is stored on this rom, it looked much better with it removed from the board. So I started looking around this area, I piggybacked a 2114 ram @ F8 and things looked much better, leaving the ram in place and power cycling the board completely fixed the issue.
I replaced the bad ram and made a new jamma adapter.
The colours are now correct, repair complete.