Are the differential carriers the same between the AT and MT?
 

I'm looking at getting a new final drive and might buy a used rear end to install it into to cut down the downtime. There's a bunch on ebay that I'm looking at but are the AT's unit the exact same as the MT's? I'm under the impression they are and the only difference is in the transmission itself.

Also, has anyone ever posted a dyno graph from a car with a new FD installed?

Yes they are the same.

The only difference in the dyno graphs would be the torque. The wheel torque is calculated as Torque(engine) x gear ratio x FD ratio.

When you do pulls on a dyno you would ideally want to use the 1:1 gear which is 4th for automatics or 5th for manuals. This in turn would mean that the only value that is changing in the wheel torque equation is FD ratio. Example: a switch from a 4.1 to 4.8 would yield 17% increase in wheel torque assuming no other mods/tunes.