I am still unable to adjust the tone on the humbucker, is this normal in a HSS setup?
If you have standard strat wiring, yes. The standard strat wiring does not have a tone pot on the bridge pickup. If you don't like this, you can wire the tone pot as a master tone pot for all 3 pickups.
2nd position (humbucker & middle) sound very nasal, is this normal or is this out of phase or something?
It could be out of phase or you could have the coil closest to the bridge as active coil. Do you have a multimeter? If so, do the following: plug in a guitar cord and put one test probe to the tip and one probe to the ring. Take some needle nose pliers (or a screwdriver) and put it on top of the middle pickup. Select the middle pickup on the toggle switch. You should now get the ohms reading for the middle pickup. Now, remove the needle nose pliers and watch the multimeter. Does it go up or down (or right or left)? Now do the same with the bridge pickup. If the meter goes in the same direction they are in phase - if it goes in different directions they are out of phase.
If they are out of phase you can either
a) swap the red and black wires of the humbucker, or
b) swap the wires on the single coils (this may be the better way if you got the coil closest to the middle pickup active in split mode).
Good luck,
Stephan