Beveled RG's looks really cool!
For the bridge pickup, you say your harmonics are not getting picked up enough, so why not try a Seymour D. Blackout?
There're supposed to have all the harmonic content of EMG's, without being overly compressed and sterile. (Sorry EMG fans)
I have no idea how to wire that with a PAF Pro in the neck, but it's probably possible
Also, I'm not sure that it will work with the Mega-switch.....
Anyways aside from that, I have a JB in one of my guitars and it's a wonderful all-rounder with great harmonics.
How about an Ibanez S style series output jack?
They look pretty sweet and the lead never gets in the way.
http://www.lifeismusic.co.uk/Products/vide...20zr%20trem.jpg
That's what I'm talking about
Will keeps tabs on this build.