Does anyone know if there would be any major problem(s) with putting a 2007 duramax / allison setup into a 2001 truck. Also would be changing pcm and tcm.

You will be changing the ECM, BCM, cluster, part of the wire harness and a host of other computer systems as well. The 01 and 02 trucks use a different computer language to communicate between the modules. You may have to change the airbag controls, EBCM and heater controls as well. Without a complete donor truck, I would not attempt this change.