Sorry for not replying sooner. The base mission files were in a different area of the assets and I totally forgot that I didn't write a script to move them if the stock map was selected. Copying the lua like you did is correct. (I generally just swap out the stock maps and use the stock mission).
Remember if you're using this method, and using it as an addon map, you want to put "ReadDataFile("dc:\TAT1\Tat1.lvl")" or whatever, instead of what the main mission has. (DC: means "Downloadable Content", and the game has a method of determining the mission file if using the addon folder.
It seems like you've got it right where you want it as well. If you need help, don't be afraid to ask.
Remember if you're using this method, and using it as an addon map, you want to put "ReadDataFile("dc:\TAT1\Tat1.lvl")" or whatever, instead of what the main mission has. (DC: means "Downloadable Content", and the game has a method of determining the mission file if using the addon folder.
It seems like you've got it right where you want it as well. If you need help, don't be afraid to ask.