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I have a 73 F-100 that has developed rust (quite a bit) above the sunvisor on the seam, and also behind your head in the drivers side above the rear window in he V pocket.
First I can't figure out how water would get there. The roof is intact, no holes.
Second, could I cut that out of a donor truck and replace?
Sounds like seams have started leaking. If it's not too, bad clean out the seam material and weld it up to prevent further leaks. Or you can install some new seam sealer. Transplanting a new top is a lot of work. In some cases users have replaced the complete cab from a donor truck.
Once you have it repaired I would spray some epoxy primmer over the repair or the complete top, then spray some 2K primmer on top the epoxy. You can sand the 2k, but it's not recommended to sand on epoxy. Have them different color so you know which coat your working in.