It looks ok to me, certainly the neck looks genuine, not 100% sure about the body but I wouldn't put my mortgage on it being a fake, the Fralin pickups are excellent and IMO better than the standard Fender one, I would be a little suspicious over the pots and pickguard as I would expect the control area to have some shielding...but again that is only from my experience of P basses and I have never owned a Jap 62 reissue!
A good few Fenders have different holes in the scratchplates / bodies that don't make a lot of sense, my 50's classic has holes in the scratchplate but not in the body, my 50's classic roadworn has holes by the bridge for a cover but doesn't come with them as standard!
If you like it then it's a good one if you don't, sell it on