Compared the two MAME ROMs.
The UBB version (parent ROM) has 3 files that are marked "UBB":
* 065-ubb04.10d
* 065-ubb05.10f
* xmen_ubb.nv
The AEA version (child ROM) only has 3 files:
* 065-aea04.10d
* 065-aea05.10f
* xmen_aea.nv
If you look on pg 10 of the manual (pg 11 of the PDF
here) and trace straight down from the word "JAMMA", you see two ICs labeled "065*04" and "065*05" with fine print beneath the ICs reading "10D" and "10F", respectively.
Looking at the pictures you posted earlier, these two ICs are socketed, so you might be able to swap them from one board to the other.
I'm not sure about the .nv file.

I assume it's a non-volatile RAM, but not sure which IC is related.
Scott