After about 20 hours of data crunching in RegiStax, my animation is finally complete!
http://itee.uq.edu.au/~davel/JupiterTransit.gif (fast version)
http://itee.uq.edu.au/~davel/JupiterTransit-Slow.gif (slow version)
The animation starts at 11.00 pm and finishes at 3.09 am. The moon closer to the equator is Io, and the one at the bottom closer to Jupiter's south pole is Ganymede. Ganymede also transits over the Great Red Spot... "action packed" according to Clayton/Rob
The seeing varied from none (total cloud cover) to pretty good. There was only "pretty good" seeing for just over 20 mins during the entire evening

Each frame was produced with identical settings by stacking ~ 2 minutes of video taken at ~ 10 minute intervals. Here's the raw 2 minute video clip with the best seeing of the evening:
http://www.youtube.com/watch?v=80YkqLeS228
Technical details: William Optics FLT-132 on NEQ6, 5x TeleVue PowerMate, Canon 5DmkII. EOS Camera Movie Record in 5x crop mode at ISO 800 and 1/30 sec, best 10% of ~ 3000 frames for each video stacked in RegiStax. Aligned, processed, and animated using Photoshop.