Hi thedude (lebowski I presume?

),
Can't really comment on your set up as I haven't used the cap set up though your occiloscope shots are interesting as they show something a single coil occiloscope shot doesn't.
Since no one has said anything yet here are a few of my observations:
as the voltage induced by the magnets increase you can see there is a slight dip in the rate it is increasing at around the point the opposite coil fires. This shows the slight delay between the transistor turning on and the coil becoming fully energised. The dip is caused by the rotor magnet's attraction to the core after it has passed the center mark and momentarily adds drag on the rotor. Probably not significant but interesting to see.
also your "blue coil's" flyback voltage isn't dropping as low as your "red coil" because it is staying on longer and so the voltage induced by the magnets increases to a higher level before the coil discharges.
and the flyback voltage on your red coil is much briefer. Probably because the current is being cut off before the coil is fully energised. This seems like a good thing as less current is being wasted.
out of curiosity... why have you tuned your coils to fire for different lengths of time?
I'm afraid I can't view the videos on your site

Maybe because I am using Opera.