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.
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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