The trailer had rust in screw holes that held DIY plexiglass covers for the windows. We took those out since ventilation is important for a horse trailer (hence the reason I like these stock styles). A horse can always have a fly mask on and a warm blanket if needed. I may in the future look at removable screening though....
The worst seam, as stated earlier was above the tack room. Seam tape for RV's was utilized along with a polymerized coating for the roof.
The process was pretty simple, path the seams and bigger holes (from a hay rack not rust) with the fabric and polymer. Then apply the roof coat to the entire surface once everything is dry.