If it can't be threaded in, you can either take it to a luthier and see what he says (make sure you get an estimate or quote BEFORE you leave your guitar there.. lol) or......
- Remove nut and first fret. - Surgically remove the first part of the fboard. - New rod... =\ - Stitch it back up.
Major surgery.
Let's see if we can get any other ideas going in this thread, though.
I think if you can push the rod back further into the neck and you can still use the truss rod to adjust the bow in the neck then you're fine. I'm not sure what truss rods Jackson uses, but with the ones that I use that aren't anchored the truss rod could come out depending on how it was installed.
Try giving it some relief. If the neck actually follows the rod, you're gold, so just put the neck straight again and there's no problem. You'd think, though, that if there was enough pressure from the rod, it wouldn't move very easily.