I learned that this was the way it works the hard way. Having to go back through and repair every thing is just as time consuming as building it in the first place so now I frame one side and put the load bearing beam on and just roof that beam which protects every thing underneath it. Then I put up the next frame and beam and roof the beam. If I'm going up another floor then I frame up one the next floor and repeat the roofing. Once i get up as many floors as I'm going I put the roof completely on as it will be for the rest of the time that base exists. After that I put walls and floors (and anything else I want) in. No rain damage that way though its a bit more of a pain to build it that way.