Water noodles! What a great idea. I can see cutting them to shape, putting on some sticky spray, wrapping them with felt, and velcroing them into a case. Excellent.
As to baritone gigbags, maybe the best thing is to wait until you've made it, then measure it, then order a bunch of bags at guitar center, then go to to guitar center with the git, try them out and keep the one that works. I did that once. It was kind of weird but it worked.