Vibration problem and much rougher ride since collision repair done

What is your question?

I have noticed the very irritating vibration (in both seats with it worse in the front passenger seat)especially when our 2008 is idling with the brake on in any position but park. It vibrates to a somewhat lesser degree when it is being driven. In addition, our CRV gives a much rougher ride. The repair was a major one with "certified" after-market parts required by our insurance company. I have read that many of the after market parts may not fit together well with the manufacturer's parts and that mechanics may find ways to attach them--sometimes through bending or drilling new holes, etc. in order to attach them. I wonder if our car has changed due to this issue. We are also looking into things such tire air pressure, condition of tires, shocks, struts, etc. and anything else that is imagineable. The service person at the Honda dealer said that the computer cannot be recalibrated to lower or increase the idling speed and that there would be warning signs on our dash if anything else was amiss, etc. He compared ours to his perception of "Honda CRVs in general". He wanted me to agree with him that our car is now very satisfactory. The only problem with his generalization is that we KNOW OUR CAR and that we HAVEN'T gotten the car that we know--BACK. If anyone out there has ideas about some other options for us, I would be very GRATEFUL! I have a back problem that is aggravated by more than minor vibration, so this is pretty urgent. We don't want to have to sell our car, which is now just 3 years old.