So a bit of a further update, I am hoping this is now fixed but time will tell I guess....
So I decided to rip the board out of the cab and go balls deep with some contact cleaner to see if that helped.
I removed the board and after pulling it out totally I noticed where the IDE connectors are that plug the cart slot into the board were not seated fully, they had sagged in the center slightly (so this may of been the actual problem?)
I pushed them in and then continued with the electrical contact cleaner and then a final scrub with one of those NES cart slot cleaner card things (which I had used a few times before)
Those contacts are now looking like new but to be fair they were not bad to start!
After reinstalling the board and powering it up with the NGSD in the slot I also tuned the PSU so it now has bang on 5V at the Jamma edge going into the board but to be fair it was only a tiny bit low at 4.96V to start with.
Anyway so far so good no errors, Left MOTW playing through its sequence for 15 mins with no issues where before it would always error out within 30 seconds or so.
So with that I am hoping this is fixed and I will have no further issues, Time will tell so assuming all goes well i will report back with good news in a few days
Thanks for the assistance thus far guys.