I had a feeling that extra blue wire might be for the antenna - the pin diagram I found for the montero shows an extra antenna wire but what threw me off is that it is bundled with the group that all goes to that smaller harness and that the harness has an open spot.
The only pinout diagram I could find was for the same 9 and 5 pin connectors but it basically was just "pre 98" and "after 98" - but as you mentioned, there must be some differences just between the years or even models otherwise the 1991 factory radio from a 3000gt would plug into my 1991 harness for the montero and work just fine. The plugs do match but it doesn't work, so i'm guessing at the very least the positive power is in a different pin location.


*Edit*
I think I may have made a little bit of progress in figuring out the wiring - I still haven't found a specific pinout diagram for the 91 Montero or the Model MB649778, but from what the internet says is standard wiring on older mitsubishi models it looks like they're supposed to have BOTH positive and negative speakers wires on the 9 pin connector and then the power wires and any accessories on the 5 pin. But the diagrams I've found for the radios that would have come in stealths and 3000gts (which is what mine is from) show only the positive speaker wires on the 9 pin along with the battery and ignition wire and then only the negative speaker wires are on the 5 pin.

But I'm still left scratching my head Here's what I've got on the CAR SIDE of my harnesses:

5 Pin Harness: Black wire with Blue stripe x2
Black wire with red strip x2
nothing in the lower middle spot

9 Pin Harness: Yellow wire w/green stripe
yellow wire w/red stripe
red wire w/white stripe
white wire w/red stripe
white wire w/blue stripe
Green wire w/white stripe
Blue wire w/white stripe
Black wire w/yellow stripe
black wire

And there's gonna be one connection on the 9 pin on the RADIO side that won't be needed according to the diagrams I found - which i want to believe are correct because it would explain the missing terminal on my radio in that connection slot.