Pre Runner Shakes After Wreck

I have a 99 pre Runner.About 2 years ago, I flipped the truck on its side after getting rear ended. After the wreck, I tried starting the truck and it sounded terrible. The whole truck shakes as soon as I put it in gear or when it is idle with the a/c on. When I drive on the highway it seems to drive fine, but when I slow down, it just starts to shake again. I took it to a couple of mechanics, but they don't know what's wrong.They said the fly wheel, motor and transmission mounts are fine. They said they could tear into the transmission, but it would cost me about 500, just to see if there is anything wrong with it. The truck was considered a total loss but I managed to keep it( with a clean title), get it paid off and get the body work from a friend for a mere $800.00. Do you guy think I should let them tear into the tranny or can you give me any other ideas as to what may be wrong? Thanks in advance for any help

Why didn't you total it out and get a new one. Serious wrecks will almost always leave a vehicle with some "phantom" or mysterious characteristics.

You could tear the whole truck apart and never figure it out.

well I couldn't afford another payment as I was sarting school. The truck has been running since, and I have put about 35000 more miles on it. I still trust that it will last me, but I just get annoyed with the vibration