RunUO does support all the map files (and duel facets for that matter), as does some versions of Sphere, as I understand it.
Yes, First thing, you would need to use an EMU that will support another map, besides Map0.mul.
Second, you would need to make your new map.. One thing though. Should you make one to replace Map2.mul, you need to be sure your new map is the same size as the Map2.mul
Third, you would need to use Dragon to make your new map.bmp, on a Map0.mul. sound like a long process? well, not even close to finished.
Then, you would have to use that map on the Map0.mul in game, to do your building, Since there is no program that I know of that will freeze your statics *.wsc files onto a Map2.mul (if ther is one, let me know, since i have yet to try to freeze onto one yet.)
Now then.. lets say you have completed the entire map on the map0.mul.. then you are ready to use UO Copy to simply copy the map from Map0.mul, to a new Map2.mul / statics2/staidx2.mul files
fun stuff
** Its late here, I am sure i may have left stuff out, and possibly are some programs that i have not used to make things go smoother. If you can freeze to statics2/staidx2.mul, then that would make things easier, at least as far as i am concerned. Simply because you could put your new map/statics2 files in game right off, and work with out needing to hog the server with a map0 just to build on.