There's nothing about the wiring in your guitar that would give you any problem installing any kind of pickups you like. Having your guitar's body routed for a Jaguar/Jazzmaster vibrato system seems rather extreme, but I suppose it's do-able. You might consider just getting a finished Jaguar body from Warmoth, or someone like that, that's already routed for a standard Jaguar vibrato system, and even, for that matter, routed precisely for filtertrons, and whatever switching/control system you need. It might not end up costing much more than having someone competently rout your existing guitar body, anyway.
