As others stated, the missing piece is probably the source of your vibration issue. Other than that, driveshaft out of balance due to punishment maybe. Big truck shops usually have shaft balancing equipment and last one i had done was under 300 bucks with new u joints installed. Made a huge difference to the vehicle.
Here's a pic of the stock torque arm trans mount. I will be modifying it shortly, will post pics in my journal. I am using the stock rear end for now with the factory tork arm tho.
I hope u find a solution to your problem and keep the car!