crankset compatability I am wondering if I would be able to run the 105 5800 crankset with my 9 speed ultegra 5600 shifters/rd?  I don't have the funds to do the whole groupset at once, and I believe upgrading to 11 speed would also mean that I need to get a new rear wheel.

Some more info / related questions:  I have an 05 roubaix that has Ultegra 5600 Brakes/shifters and cassette/RD, and an fsa gossamer 52/39 crankset.  the front derailleur has 3 positions although I just have 2 chainrings.  the front derailleur shifts pretty terribly and the chain drops frequently when i shift down.  do most front derailleurs have 3 positions even when there are only 2 chainrings?  I set it up so that I can use the middle position to get away with some cross-chaining, but should I be doing this at all?
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.