As somebody with a lot of time and energy invested in Bigshell and the other maps you're referring to, I can confirm that MCEdit is exactly what you'll want. It's trivial to load the existing maps, select all of the terrain on which actual construction has occurred, and then export it to a file.
Once you've got files for each of the maps you want to incorporate, it's probably best to just start a new map in Creative mode and fly way out away from the spawn. You might want to survey a pretty big cross section of areas so you can find terrain that nobody's going to mind getting supplanted by the old content. While Kort Pleco states above that MCEdit requires the area to already be explored, the version I was using had some tools for filling in ungenerated sections, so it shouldn't be too hard to take a map that has some holes in it and import the files from above.