Jason.. Just a couple of things...
1st.... Just to keep the record straight for historical accuracy. As I was the lead mechanical guy on the Shorty D&RGW Reefer 39 restoration, All 4 truss rods I installed were brand new and made to fit Reefer 39.
2nd... Having restored 2 stock cars for the DRHS... The very first thing you need to do is... Have the roof boards milled ( Tongued and grooved ) and then rack them with spacers to dry out for at least a year or more. We did not do this, and after 3 mts, the shrinkage opened up gaps between the roofing boards, We calked and repainted, only to have to do it again 6 mts later. We were lead to believe that the wood was dried. And maybe so but not enough.
The reason that the top sills on stock cars are all rotted out is the leakage between the boards allow the water to run down, and settle on top of the top sills, and rot them out. If in the winter, you get a freeze thaw cycle until the sill dries out... If in a wet environment that will hasten the rotting of the top sill. The diagonal side truss rods are only held in place by a piece of metal that is torqued down by the nuts on the bottom of the outer sill, and any tightening only hastens the crushing of the dry rotted top sill.
Contact San Juan Timberwrites in Arboles CO, they cut and milled our 3 new top sills in one piece 30' long fir, from vintage reclaimed timbers. Well seasoned.
Dave Taylor