Ok, moving a bit forward with all this. Figured out a few more things including flat fielding and dark subtraction.
Found the log files and the fps on the night was pathetic. ~1 to 3 fps. No surprise I couldn't even separate those stars. There's just barely a hint of them as a line at 11'oclok from the brighter one but that's about it.
I managed to get a sustained 25fps today on the bench with res ranging from 960x960, 1024x960 and native 1280x960. I went from under 1ms exposures up to 10ms no problem, from 100ms onwards the fps quickly drops to 15 then 10fps. Also played with the RAM buffering settings. Didn't seem to make a big difference. CPU usage is 50% on the dual core, HD speed is fine, so I can only conclude the bottle neck is simply the USB2.0 connection. A faster lappy or more RAM would make jack squat difference. I did the test with a 1.5m cable straight to the notebook. Tried 3 various ports. Killed all the background processes to make sure FC was the only thing running. Same result.
So if I can get around 20fps on the night I should be ok. Just waiting for another clear night now.