Your Questions:
how I can best seal up the bolts in the roof: I would use short blocks of wood, maybe a 4x4" and use the bolts to attach. Seal around the bottom (you'll need to cut to match the roof) and you've made an effective plug. If the bolts come out easily, turn them upside down to preserve the threads. Normally we plan to replace bolts during a full restoration anyway, but that is an expense you need to decide to do or not.
Interior-Leave alone or if the only good option is to repaint? My opinion is that if you don't need paint to protect it, leave it as is. It's always fun to see the insides of these cars.
door hardware Yeah, original hardware is always a problem. You'll have to scrounge around for that; I know I helped scrap some cars in Manassa just so we could get hardware for converting P-Boxes on the C&TS. If photos aren't available, I may be in a spot to get something similar (eg CRRM-Golden) soon.
The first year I volunteered in Chama (pre-FoCTS), we worked with some retired Rio Grande (Grand Junction) car shop people. I made the mistake of referring to a roof walk, and the ex-foreman jumped all over me in a friendly way and explained that Rio Grande cars didn't have roof walks. They had "Running Boards".
Bill Kepner