[cruiser_guy]

If I were you I'd get a "bung/boss" or whatever you want to call it, welded onto the loop off your stock manifold going to the turbo and put your pyrometer sensor right there and call it good.

If I were going to use multiple sensors I would be measuring temperatures of the air entering the engine AFTER being compressed by the turbo before I'd be messing with individual cylinder readings. With your flipped manifold the individual readings would not be accurate anyways as you don't have a separate path from each cylinder to the turbo.