What year TJ?
In most states, inorder for the vehicle to 1. maintain ODBII compliancy and 2. further pass any emissions, the motor needs to be from the same year or newer model, so for example, if your jeep is a 2003, 2002 was the last year for the 350 and was found in the F-body cars as an LS1 (and are harder to find and cost a lot more $$) 2000 was the last year for the vortec 350 in the 3/4-1 ton trucks and 1/2 ton tahoes and suburbans (and GMC counter parts) so a legal swap may not be permitted.
Also why a TH350, with a 700r4 with deeper 1st gear and an overdrive for the same cost it seams silly to run a TH350. If it were me, I would source a 5.3 LS motor and run the 4l60e trans. The 4l60E is the same exact trans as the 700r4, with a beefier 3 piece case and computer controlled shifting for optimal milage and performance.
You can get junk yard motors and trans for about a grand, complete with ECM, trans module and entire wiring harness. You will get a drivetrain that is far superior to a 350/350 combo. Plus, throw a cam and a hot tune at a 5.3 for about $400 and you can make well north of 350-400 hp easily.