Have you considered a roof coating like the kind used on mobile homes. Although my experience is limited, we used the stuff on an old camper that we had as a temporary structure while building our weekend home. The thing leaked like there wasn't a roof and the coating sealed it well enough to last the 4 years we used the camper. The stuff isn't cheap but I think with your panels nailed in the valleys that you will have a hard time stopping the leaks with caulk.
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