The singles will come with Fender-style covers (black, white or whatever you choose) and I'd recommend keeping them on unless there's no room in the pickup rout - exposed single-coils are pretty fragile.
Not sure about vintage stagger or flat profile - I'd probably stick with whatever is standard for the single-coils you choose (Tim knows what he's doing!

). And I'd go for RW/RP middle and stock neck (or vice versa) - that way it's hum-cancelling when both pickups are on. If you buy an HSS
set, I believe one pickup is RW/RP as standard.
For the spacing on your MG bridge pickup, I'd measure the
actual spacing between the two "E" strings over the bridge pickup (where the polepieces would be if there were any!). Then choose whichever spacing is closest - 50mm or 53mm. The neck pickup should always be 50mm.