If it is present, then I would go ahead and remove it. I would think it's already omitted though.
If it's actually a populated pin on the PSU, then they are using an out of date specification, but it shouldn't harm anything if removed since it's not connected to anything anymore anyways.
Don't forget the molex pin extractor. I know some people love their safety pin kludges, but having the actual proper tool is useful.
You should also get a heat gun for the heatshrink; again, a lighter will do in a pinch, but it's worth it to do it right.
You can do the same with the sleeving: cut them at an angle and join them in the same wire-Y, use heatshrink.This is really hard to achieve when you want to sleeve them as well
Hopefully someone here can verify if indeed HDPlex removed that -5V pin.
I bought an actual Molex crimper