Pictures! (worth a thousand words?)
OK, I got it out and took some pictures. I must say, the drawings in the manual are pretty bad. Perhaps if I had the original manual (not the PDF) it would be better, but I'm not sure.
In the first picture (2552) you can see the entire assembly. Note that I do NOT have the jamma filter boards installed at the moment.
In this picture you can see the two game boards stacked one on top of the other, and on top of them two smaller boards (the one on the left is the JSA3S board, the one on the right (mostly hidden behind the metal support) is the CLARN board. The ribbon cable is pretty much behind the metal support in this picture as well. On the outside of the shell you can see the cables for interconnect to another system.
On the left hand side of each of the game board, you can see a spot for a board edge connector to plug in. That's where the controls connect (via a short board that appears to just have some filter caps on it). These appear to be more or less standard Jamma connectors.
In the second picture, you are looking in from the left side, to try and make the ribbon visible. It's right behind the metal support, and I was wrong in how it runs - it runs from the LOWER game board all the way up to the CLARN board. Since the CLARN board sits directly on top of the UPPER game board, it appears to direct connect with headers instead of a second ribbon. Notice that the ribbon has a big grey thing clamped onto it - that's an inductor and is usually used to suppress RF noise.
As near as I can tell without a working unit to look at, the ribbon cable behind that metal support should go where it's seen here, and there are no others.
I note that there is only one JSA3S board (even though the manual says '2 places'), and I hope that I'm not missing one.
Good luck!