So, ultimately you'd end up with a new neck, new pups and what's left? Assorted hardware and the lump of wood called the body?
I would not call that modding a guitar any more; that's building a new guitar and scavenging some parts from the old one you have, and that to me seems just wasting a good base guitar to mod into something entirely different and the hard way.
Put in a 100 bucks more and get all the new parts, build an all new guitar and keep the one you have as is, and just give it a fret job etc. to make it a better player. Or, even better, buy a used, battered Jackson that's a bit like the one you have, and mod that to your heart's content.
Dee
"When life's a biatch, be a horny dog"
Amps: Marshall JVM 410H w/ Plexi Cap mod, Choke Mod & Negative Feedback Removal mod, 4x12", Behringer GMX110, Amplitube 3/StealthPedal
Half a dozen custom built/bastardized guitars all with EMG's, mostly 85's, Ibanez Artwood acoustic & Yamaha SGR bass, Epiphone Prophecy SG, Vox Wah, Pitchblack tuner plus assorted pedals, rack gear etc. for home studio use.