The 3.6l uses the same pcm as the 2012 and newer Hemi. The 3.6l v6 Jeep also uses the same 5speed NAG1 5speed auto that is a common swap. Just swap the bellhousing.
Hardly no aftermarket suppport.
The OP already has a Hotwire harness to use as well as a Quicktime bellhousing for the TKO.
Diablosport and Hptuners both offer tuning software.
Edelbrock and 3 other vendors have bolt on superchargers and 3-4 others offer Turbo kits.