If you're running six buttons, you are definitely going to need an additional harness as well (Jamma is 3 or 4*).
RE: Missing wires ... best guess (not having Jamma pinout handy) is it is missing Coin Counters,lockouts, tilt and possibly more.
I find it interesting that the second harness cites "fully stuffed with wires in all slots" ... IIRC, Jamma has at least 6 pins that are empty (including the key slots). Are there non-JAMMA boards that use a 56-pin edge connector ? I guess that would make sense then.
Cheers.
* 3 is "official" ... some games run button 4 through the edge connector, though.