Cool stuff, you should think about how nice this sounds and not how hard it is to record. Agree with James that some structure would be good, but on the other hand, who cares, ANARCHY :D
A tip: most sequencers can be remote controlled and allow "punching in" into a recording, which basically means pressing the record button during a running playback.
If you'd setup a simple midi remote switch, you could play along to the tick or a backing and while being in the playing flow hit the record button. It's easier to start recording like this as you don't have time to think about the fever while being in the playing flow ...
And for sure, the other suggestions are even better. Normally when I play live, the first 2 or 3 tracks are normally cr@p. The worst thing is that people don't even realise, which means it doesn#t matter how you play anyway :)