that Sys12 document in MAME is mine, done over several years

If you look at most MAME source files you'll see similar documented info about whatever game board or system the source is for, and that info was usually created by me. They are known as a "Guru Read-Me(tm)(c)(r)"
FYI, any S12 top board will work on any S12 bottom board.
a blue screen with a weird white Japanese character in the middle of the screen means the CPU (on the top board) can't see the program or the program is bad. Mainly it's a bad connection somewhere between program ROMs and CPU, but it can be a bad TSOP.
The most common failure on Sys11/Sys12 is loose chips on the top board, but since your top board is working it has to be something on the lower board.
Almost all Namco boards have bad soldering on all SMD chips (everything in this list starting at Namco NA-1 and onwards....
http://system16.com/museum.php?id=7) so I'd start by re-soldering the TSOPs on the lower board, which contain the main program.