crankset compatability
11 speed chain rings will be slightly narrower than 9 speed. So they will work, but it's not an ideal pairing. You should be able to keep your rear wheel and replace the 9 speed cassette with an 11. The dropout width hasn't changes, the gears have just got thinner.

Not sure what you mean by front derailleur having 3 positions. It swings through a fixed distance, it is the shifter that determines if there are 2 or 3 indexed points to stop at. A 3 speed shifter isn't going to work well with a 2 speed chain ring. But you try adjusting the lower limit screw to stop the chain dropping.