as a beginner, I would suggest not getting a Floyd Rose or a trem of any kind. A hardtail or Tune-o-matic bridge will be FAR less frustrating to deal with - as far as tuning, intonation and general action/setup issue go.
I also think that, honestly, if your a total noob at guitar, you should probably wait on Warmoth, before you drop a lot of cash on a guitar. You'd probably be better off getting something less expensive and learning to play on that. The reason most people get Warmoth stuff is they want to be able to make a guitar that they can't really find anywhere else. You don't even know what you want yet. You'd probably be better off going to a music store and trying out a bunch of guitars and seeing what feels and looks good to you.
as for you questions - - when it comes to pickups, everyone has opinions. again, it really depends on the sound you're going for. a lot also depends on your amp. I don't think you can go too far wrong with any kind of pickup - -but if you're picky about tone then you're got to do some research and find out what different characteristic different type of pickups have. You could probably get some decent GFS pickups for cheap.
as for a pickguard - just get whatever kind you want...