New tranny, new problem
I would check all of the mountings, Torque arm, trans mount (check for tearing, you'll have to pry between the trans and crossmember to see it/feel it). Check the exhaust where it bolts to the tailhousing. Sounds like what my trans mount did when it broke though, I'd start there. Check to make sure they tightened the trans mount as well, they may have left the nut out or something stupid. It happens sometimes....
Failing all that, could be internal but it's not likely.

