Reaptress

I am at a loss. To make a long story short, after tons of disappointment and shop to shop problems.. I had my transmission rebuilt, my catalytic converter and manifold replaced and the issue still exists.

My car has been jerking a lot more than the usual slip / hard shift between the first gears as a honda does. It's a violent jerkiness, too. I have taken my car back and forth from the transmission shop, and for awhile my light came on for the catalytic converter. Recently replaced the cat and the manifold just incase cause there was an issue of manifolds cracking. Really dissapointed it still was jerking, drove a lot better but still poor performance and jerkiness. I recently got hit not too bad in the parking lot of my job and the jerkiness stopped... It's been a week and now it's started happening again the other day a little not as bad but it's still there. Is something out of whack? No lights are on and I am under warrenty for the transmission, but this is becoming trying and I have no idea what is wrong.... Any tips?! Is something out of alignment? So confused!!!!