Grant, When we (DRHS) restored 04432 bunk car..... We cheated a bit on the roof, for the sake of long term preservation. Prior to our obtaining the car, a "New roof" was laid on the top, consisting of 5/8" plywood, covered with tar paper and a layer of asphalt roll roofing. The Roll roofing had gone bad and was missing in places, and the tar paper was the only watertight stuff. but it too was badly deteriorated.
Having dealt with the big problems of water damage to the top sill on other cars we restored, It was decided to leave the historical incorrect, but sound, plywood in place, as 04432 had a beaded wood ceiling throughout and it was "Out of sight". . We felt that the very best way to "Seal" the roof was with "Ice Block", ice dam underlayment ( made under numberous brand names). This stuff is a bit@h of stickie stuff and a pain to work with..... But it is the ultimate water seal. It is self sealing for punctures and will seal around bolts that go thru it. Not the cheapest stuff, but the best long term sealing underlayment. We covered the entire roof in it. We then put the traditional 1x T&G roof boards over the entire roof. Applied yet another layer of the ice dam material. Then used the red roll roofing and nailed that down in the typical D&RGW style, with the edges rolled over the facias and nailed.
When we received the car, there were no "Through bolts" for the running board braces, only lag bolts into the roof. We had several of the roof walk supports to use as a pattern, and I cut the "V" on the band saw to fit the roof profile, and these were spaced and bolted down in recessed holes, All these bolts were covered by the running boards.
Just a hint of how we did 04432....