I haven't built the kit - or even seen the inside of the box. My guess, though, is that when the model's finished the view of the interior will be pretty murky. Your idea of painting the interior surfaces with a wood color sounds like a good one. I suspect the generally "woody" appearance, seen through the windows, will be enough to look convincing.
Regarding the clear plastic parts, two suggestions occur to me off the top of my head. One - paint the bulkhead interiors first and, if there's sufficient room, rely on the glue at the top of each clear piece to hold it in place. Two - paint the bulkhead interiors first, let the paint dry thoroughly, give it a coat or two of flat finish, let that dry thoroughly, and stick the clear parts into position with white glue. Our friends in the aircraft realm use white glue for mounting clear parts frequently. It obviously doesn't have the solvent effect that plastic cement does, but it holds well enough for most purposes.
I've seen pictures of the box for that kit. It looks like it has the potential to be a nice, slightly offbeat model. Good luck.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.