I feel your pain - I too was terrified of the electrics but eventually, we have to deal with it. I did mine before installing the engine but I probably could have waited.
Strip out the old harness - mine was full of splices and non-standard-colour jumpers etc. so it just confused the issue. I then located the new harness in the more-or-less correct position with tie-wraps. As Mr. MoMo says, everything is colour-coded so it's hard to go wrong.
FWIW, I started at the connections beneath the left sidecover - starter solenoid, VR, indicator relay etc. That helped with the positioning of the harness. Then I went to the bundle aft of the steering stem (handlebar switches etc.), then the headlight bucket connections, tail-light and ignition coil. Depending on your geographic location and the source of your harness, you may have to plug in a few jumpers (i.e: my left handlebar switch had no clutch switch so I had to jump the green/red to ground).
You'll need an accurate wiring diagram. Looked like a plate of spaghetti to me until I sat down with a beer and a magnifying glass and really looked at it, comparing what I saw to what I had.
In the final analysis, you just have to grab the bull by the tail and face the situation
. It isn't as difficult as you may think and there's lots of help on the forum - I know these guys helped me out many times when I was confused!!
Regards,
