Wow. Beautiful game, seems very polished.
I do think the simulation is a little hard to control--it is kind of the point of QWOP, but it makes it really difficult to design and control things. Dragging the blob creature (for example, to right it) feels very slow. The muscles did feel very gooey, though, which felt nice.
With regard to difficulty, I think it is hard to balance a game like this, and while I can offer criticism I can't really blame you for the 48 hours you had. For every level up to the one with the ledge, I simply used a triangle-creature, as it was easy to control and got the job done. When I got to the ledge, I felt under-prepared, and couldn't pull it off. I like to think that I'm a spacial thinker, but it was beyond me how to move something big over to the right when I had previously only used a triangle. Perhaps allowing freer level flow would have helped, letting me try out complex designs on my own within environments.
Overall, though, it looks awesome, and I really like the concept and theme matching.