With mods you drastically narrow your prospective client base. If someone doesn't like the "Jem" scallops, they're gone! Pickups are always replaceable, and sometimes I'll overpay for a guitar with expensive pickups. Other times, I find I don't have to overpay, because whatever stupid Guitar Center/Sam Ash/etc. employees don't understand that the pups are worth some money. Stores usually view modded guitars as curses, because they know it narrows the audience. But with auctions and forums, you'll probably always be able to find someone that likes what you like.
Upon resale, I would definitely convert that killswitch to a coil cut. That would drastically broaden it's appeal. The sparkle finish chips and flakes like crazy. Be careful when drilling your killswitch hole, and be sure to countersink it afterwards! On both sides!