I'm not sure exactly what you're referring to, but the amount of work involved in that kind of port will depend on the content you want to use and the organization of the original. For instance, in SOA 2, we had originally renamed all of our files to reflect Star Trek-specific content. To better adapt to constant patches, however, we switched back to using the stock game's naming conventions while using trek-specific names only for our 4th and 5th races.
If file name changes have been made, you'll have to make a lot of small adjustments in nearly every text file. If it's just some minor alterations within entity files and whatnot, then you simply have a few extra lines to add ("usesFighterAttack" and "allegianceDecreasePerRoundtrip" come to mind). Text files with different names or that are in addition to the standard compliment of files must also be added to the manifest files, otherwise the game won't recognize and load them. This includes entity, brush, color, and window files.
Things like textures, meshes, and particle effects just need to be put into the appropriate subfolder to function correctly.