find the U49 and apply a lil bit of pressure to it, it should clear the issue unless the chip has gone bad. Its not a socketed chip, if you need to replace it, you need to de/re-solder it. As for not saving the volume and difficulty, thats due to the CMOS not being in memory.
leave all your dips off except for 2,3,and 4 in bank 2. That'll give you free play

Where are you located? If you dont mind me asking, how much did you spend on the game? Theres a seller named Q*Bert_Op that sells PCBs he might have a replacement MKII for ya, I just got an MK1 from him for $60 shipped. (Now I just need to find a non Ultimate MK3 and maybe an MK4 so I can wire up a MultiKombat machine inside my MKII cab =)
I sort of regret telling you had to adjust the width coil now that its ruined, but I tried to stress you need to use a plastic tool and not a metal one , sorry.