Hey PwnCall, so good to see you here!
You can have as many different LevelEdits or Mammoths as you like without needing to uninstall them.
There aren't any gmax building files to be found to merge to maps, but fortunately they are just proxies, so you should be able to prepare your own building proxies without too much difficulty. You could try w3d importing each of them but what I'd actually recommend is not bothering with that and w3d importing the proxy masters file instead (poke me sometime to export it first). There you will have the proxies and the temp ground shapes. In theory this should save you the most time.