Not having a synchronized controller sounds like a major setback.
Coming from a game-hacking perspective, I would say you either inject a controller into the game using Flasm, or just decompile the scripts with Flare and create your own QWOP simulation using its rules. I don't know how feasible this is, but this is how I would approach it.
Or just tell the author what you're doing and he might help you out.
edit: Nevermind. Flare and Flasm failed to produce anything from qwop's swf file. It's definitely obfuscated. Try asking the author for an API..