I have managed to refit the neck and tighten it down. The sanding I did seems to have helped rectify the small gap that was between the heel and socket. The nut is a bit more central now, so the strings sit better, though still slightly towards the high E. I have also re-aligned the neck pup, though I have gone too far the other way, but it will be fine, certainly better than it was before at least. Thanks again for your comments and help, really is appreciated.