: I can't imagine cutting out the cockpit before it's glassed.

OMG... we don't agree on something! ;)

I do it all the time. Yes, you do need to be careful with the un-glassed wood. A new jigsaw blade helps and set the saw so there is no/little oscillation (vertical movement only). I just posted an entry on my blog showing the same operation on the hybrid Night Heron I'm working on. I did apply a seal coat to the 1/8" thick sapele. To make it easier on the saw I knocked out the few forms in the cockpit area.
http://clearstreamwood.com/WordPress/projects/2010-neytiri-hnh/recessing-the-cockpit