Using the editor you can create Mongol units in the Sengoku Jidai (i.e. non Mongol) campaigns. However, after the game starts, the Japanese clans will not be able to train new Mongol troops. What Mongol units you have at the start is all you'll ever have.

Note that I have not tested having a Japanese general command Mongol units on the battlefield. I'm not sure what will happen. So this is at your own risk.

The editor (v1.1b) is available at totalwar.org. The editor itself is 325KB in size, but if you don't have the required DLL (MSVBVM60.DLL) in your C:\Windows\System you'll need to download that too (718KB).

http://www.totalwar.org/maps/xmods.shtml