Re: new here have some questions.
i think as long as if/when u decide to sell, you're totally honest about what parts you've used, where they're from, etc etc, then you stand to recoup a good chunk of your costs.
for example, say you get a body from Nate Perle, get it swirled by Herc Fede, original edge/lo pro, dimarzio electronics throughout, MIJ/gotoh/sperzel tuners, and a 550 AANJ wizard neck, that may cost you somewhere in the region of $500-700ish. now you will never see all of that money back when you sell it, but particularly on here, people know the quality of the workmanship of the parts you've got, and what they're worth 2nd hand, and a lot of people are happy to pay "what its worth" as a 2nd hand project!
as long as you dont try and pass it off as a genuine, original ibanez, then you should see a fair price in its sale.