The grey wire might be for phase issues, which you seem to be having, but the issue is the Transition clones. The EBMM Luke III (and the Sterling that's based on it that has the pickups you're having trouble with) have position 2 and 4 being inside coils together, then outside coils together, so the neck pickup is RWRP relative to the bridge. If you're using an HSH setup, you want your neck and bridge humbuckers to have the same winding direction and polarity to work well with the middle single (unless you use the inner coil of one humbucker and the outer coil of the other). In your case I think you'd have to take the neck pickup apart and rotate the magnet 180° (so the part that used to be under your treble strings is now under your bass strings and vice-versa) and that should hopefully fix it. If it's still an issue after that, you'd need to swap which coil of the humbucker is active in position 4.