Weird bad vibration Help??

I got a 70 Mach 1 with a 351w. I decided to tear the car apart for a winter project. Pulled the motor and tranny, fixed up front suspension, painted the firewall and clean everything up. Reinstalled motor and tranny and now I have a weird bad vibration in the motor. While sitting at idle the whole car shakes. I did not remove the balancer on the motor and did no internal work to it or the tranny. I had the motor and tranny separated and was wondering if when putting them back together I did somthing wrong. The flywheel only bolts up one way. Does the torque converter have to go in any special way? There was no bad vibrations in the car before I took it all apart. The motor runs great just like it did last fall.
 
Do you mean that you installed the torque converter without lining it up with the hole in the flex plate? I wasn't aware of this when I installed everything. I will have to check to see if I lined it up. I did fine a pretty good vacuum leak. Going to repair it this afternoon Hope this does it. Thanks for the input