Did you miss the 2 stroke part? There is no suck unless you do something really clever with the exhaust pipe geometry.
expansion chamber forms part of the exaust (the bulbus portion of a typical two stoke exaust) the inertia of the exaust gas (in the bulbus section) keeps its momentum forming somewhat of a vacume behind it drawing in the next charge

clacker valve :) reed valve we used to call them

"injecting at TDC" youll have to look into that one... im assuming that you would get better atomization at lower pressure (during induction or there abouts) at TDC the pressure would be quite high with it being a deisel


I currently have it set up so that the opposing pistons are basically one unit
i think your ok in principle but i would have thought a 45degree rotation on your crank timing so that your firing one charge at a time (higher frequency vibration but less amplitued than firing two charges simultainiously i would think)

crank balancing ..... errrm.... your on your own there :) im not sure if you just balance the crank or you take some of the piston and con-rod mass into consideration