All I know as far as converting to a manual tranny is that the transmission is available in catalogs, I know I've seen it in the Quadratec catalog running upwards of $1500.00. You could probably get the clutch pedal or something from a junkyard, but be prepared for an expensive operation.
In the Quadratec master catalog or website (www.quadratec.com)they sell floor pans, and pre-fab sheet metal for specific parts of the Jeep body. It's usually listed in the restoration category. Or, if you don't want to dish out the money, you could cut sheet metal to size for whatever you want to replace, and weld it from there.
1984 CJ7-31" BF Goodrich AT Tires, Auto, 258 ci, Pioneer sound, 2 barrel Weber carb, undergoing some body work and exhaust work sometime soon.
"pop the hood, POP THE HOOD!"
- a phrase commonly heard in my garage