I don't have my Warpig yet, so I'll let someone else answer you there. For your other questions, I can give you some answers:
1) 4 conductor allows you to wire the pickups in series or parallel (much thinner sound), or split the coils. For a PRS with the rotary switch you would use 4 conductor, and in a HSS set, using 4 conductor lets you get the strat split sounds. If you only need the humbucker sound (or if the wiring path in the guitar is narrow), 2 conductor is the way to go.
2) Depends on many things, the brightness of your guitar, the type of pickups and also how you want the tone to work. Humbuckers traditionally have 500k pots and .047 mf capacitors, however if a humbucker is fitted in a Strat, most people leave the 250K and .022 mf originals in place. This doesn't change the sound too much because the combination gives a warmer tone on the volume, but brighter with the capacitor.
Another good combination is 500k volume and 250k tone with the .022 mf capacitor. This gives a brighter sound and doesn't roll off as much treble. Also BKP sell 300K which sits in the middle on the sounds.
3) There are 2 staggers that BKP make, the 54 and the vintage. The vintage stagger makes the top E & B lowest, then the bottom E & A, with the D & G tallest. The 54 has the G magnet lower and A higher than the vintage (I think). In the flat, all the magnets are the same length.
