Over on KLOV they managed to change the colour palette to work with boards with the RP2C04-0001 PPU, MBJ uses the RC2C05-02 as standard.
Out of curiosity I burnt the RCP2C04-001 set for my Super Mario Board which which uses the RP2C04-0004 PPU and the game runs but with wrong colour palette.
https://forums.arcade-museum.com/threads/major-nintendo-vs-development-mighty-bomb-jack-using-a-rp2c03b-lilman-rocks.296104/
According to the thread on KLOV you can make it work on other PPU's but you need to convert the specific special colour palette to the standard colour palette MBJ uses.
So I assume that the special colour palette below for the RP2C04-0004 PPU:-
RP2C04-0004, Special Palette 4
430,326,044,660,000,755,014,630,555,310,070,003,764,770,040,572
737,200,027,747,000,222,510,740,653,053,447,140,403,000,473,357
503,031,420,006,407,507,333,704,022,666,036,020,111,773,444,707
757,777,320,700,760,276,777,467,000,750,637,567,360,657,077,120
Will need changing to Mighty Bomb Jack's standard palette:-
All other VS System PPUs reportedly use this (or similar?) Standard Palette
333,014,006,326,403,503,510,420,320,120,031,040,022,000,000,000
555,036,027,407,507,704,700,630,430,140,040,053,044,000,000,000
777,357,447,637,707,737,740,750,660,360,070,276,077,000,000,000
777,567,657,757,747,755,764,772,773,572,473,276,467,000,000,000
VS Palette info found here:-
https://forums.arcade-museum.com/threads/anyone-working-on-vs-rom-ppu-palette-hacks.335366/
If there are arcade hardware guru's on here capable of deciphering the colour palette to make it work for a RP2C04-0004 PPU that would be greatly appreciated.