Omega

iTrader: (5)

I have found some missing wires and some cut wires in the harness I bought. I'm not totally sure what year it's from, I just know it's not a 98.

The alternator now only has the one red wire. I have read this is bad and would like to fix it.

I have no idea how the numbering sequence goes at the blue and red connector. I thought they were shown in the FAQ here, but the images are broken. How does it go?

LS1MCSS

iTrader: (18)

Try this link. It's in the swap fac at the top of the conversion page.
http://www.ls2.com/boggs/torques/99pinpcm.htm

G-Body

iTrader: (4)

The red and blue connector are numbered right on the connector. Look just above the wires, its kinda behind the grey plastic cover.

If it is an f-body harness there should only be a single red wire going to that alternator plug.