Charlie,
That fairing looks great.
Are you rolling or spraying the paint? At this point I would drill and seal the holes for the wiring, sand all the inside joints, and deck before painting. Once decked, you can then run the electrical wire (you still have to fillet the inside of the decking. I put my wires in standard automotive wraps and used looms to the hold them as close to the underside of the deck as possible (to keep dekes or anything else from rubbing against or pinching the wiring harness). The advantage of spraying after decking is that you can hit the screws, looms, and fillet holding the deck. Of course, this does nothing to better hide the boat and is totally unnecessary, but since you did such an outsanding job fairing the knees and floor, I'm sure you do not want to see white 5200 or shiny screws when laying in the boat (and yes, I took care of this trivial detail on my boat). Also, once painted, neopreen matting from chine to chine, cut out to fit around the knees works great. It is comfortable to lay, sit, or kneal on; acts as an insulator against the cold; dampens noises; and does a great job keeping heavy or pointy objects from poking though the epoxy. No need to paint under it. If you want to make it permanent, contact cement works great.
Bottom line is either way will work fine.
I've really enjoyed seeing the attention to detail of your work and hope to see her in the water soon!
Take care,
Bill