This is the way i'd do it (if I were to do such a thing). Cleanest, IMHO.

My wife's father is a pro bodyman and did this on a rolled 4-runner for her graduation present. When we talked about it he said it all came down to measure, measure, measure before cutting. Lifting the old section off and the new section on were a pain too, but do-able. The biggest time-consumer was more the re-fitting of interior pieces, grinding welds and prepping for paint. If I had a tall garage and time to take the van off the road it'd be a fun winter project!

john