Dirk,
My wife and I had a full weekend. First, we didn't just have to reseal the windows. The wood paneling had been damaged all around the loft window on the passenger side. Plus the wood was being rotted on the floor of the loft on the same side. Being the first time we tried to do this type of work ourselves, it was more of an adventure than a pain. We spent the week duplicating the wood panel itself so by Saturday it was just a matter of putting on the framing and foam. While I did this, My wife broke out all the damaged wood in the floor with a utility knife and replaced it with fresh wood. It was a little make shift, but it turned out not looking too bad. It was so rewarding when we put it back in and it matched up with the place for the window. It was even more rewarding when the window itself fit nicely and the holes matched up. Its almost unbelievable that the caulking job looks like it is keeping the water out!
Thanks again for the tips on how to caulk. Ours wasn't the most professional looking Job, but it seems to be working. Practice makes perfect. You were right about getting the mating surfaces clean. That's what took the longest. We had out first big rain last night, but the 'rader is in the shop getting new carpet and a new loft mattress. (We are so stoked!) I guess we'll find out this weekend how our work held up.
If you want I can post some pics As soon as I figure out how to do that.
Any luck with the break in hte rain?
Josh