Use the stock transmission and transfer case. Get the pilot extension for the torque convertor to extend it out to new engine's crankshaft pilot bore. I'm thinking it was Hughes that make the extension. The wires for the speedometer pickup sensor will need to be tied into the old PCM to make all the old equipment work.

You may not need the extension with the 2001 flywheel if its the flat model. The flat flywheel is used on the longer crankshaft and will mate up to the old converter without issue.