3 pin/4 pin ignition switch connector compatibility

I have a '99 VFR800 and I need to replace the ignition switch. I bought a used lock set from another '98-01 VFR but didn't look closely at the pictures and the ignition switch has a different connector than the one on my bike. My factory service manual and the ignition switch I bought only have 3 wires, but the ignition switch on my bike has an extra pink wire. Did the 2000-01 bikes have the 3 pin connector? Does anyone know what the pink wire is for, and if I can get the new switch to work with my bike?

 

I did some snooping, check out this old thread. That last post seems to indicate the pink wire is a trouble indicator for the ignition electronics:

http://www.vfrdiscussion.com/forum/index.php/topic/53885-ignition-switch-wires-1/page-2

 

I meant to post a link to that thread, it's the only place I can find that wire mentioned online. He says the wire should have no voltage so I could try to leave it disconnected or shorted to ground. I did start taking apart the switch while it was still on my bike and I saw a diode in there so maybe the pink wire is connected with a diode. I'll probably take the old ignition switch off the bike this weekend and completely take it apart to figure out how it works.

 

I got the ignition switch off the bike and the internal wiring matches the 02-09 wiring diagram. The bike was sold to me as a '99 and a VIN lookup says it's a '00. Not sure what's going on here. The colors of the wires on the harness and the ignition switch match the '02-09 wiring diagram, so I guess someone must have swapped harnesses? It looks like the 5th gen and 6th gen ECUs have different connectors, so they must have swapped the ECU too. Is this possible? Common? Can anyone help me understand what happened to this bike? Any way to tell if the engine has been swapped?