I have a waggy d44 and its not centered. Its for the rear but one side is two inches longer than the other. I though all the axles '80 and up were centered?

2" isn't going to hurt anything and that is considered centered. I've got one of the offset ones out back and its over a foot to one side. Most axles are a bit longer on one side so the pinion will be centered.

so if i make the correct brackets for the jeep its good to throw under it?

Should be.