whoa, there is a lot to read here.. My 2 cents:

The simplest way to improve pedal stroke is to improve the "sweep" at the bottom; mash down and focus on pulling the pedal back until the up begins... IMHO you'll get way more out of this than worrying about how hard you are "pulling up".

If you have tight clips or clipless pedals you can worry about the upstroke after you get the sweep down, but at this point you are working on pushing in a nice circle rather than mashing.