I ripped my guitar apart and replaced everything original. Only problem now is that I do not know what to do with the jack, I had one EMG in the bridge and a passive in the neck. I'm not really sure what to do, I still have the original mono jack if I can't use the one that's already hooked up.

I would post a picture to show what it looks like but I have no idea how to upload pictures from my phone
Nothing wrong with using a stereo jack. Don't leave the wire that was connected to the ring lug hanging loose. You can bridge it to the sleeve if you like, or just clip it.