Could they have done something wrong?

I took my car to Pep Boys because all the water had leaked out of my coolant tank. They kept my car for two days, claiming they needed to replace the intake manifold. When I picked it up, I put it in "Drive, " and the whole car jerked violently. I should have just stopped right there, and handed them the keys back, but needed groceries, so I drove home. On the way, I noticed it was jerking every time it changed gears, which told me, "Oh, crap. Something they did has messed up my transmission." THEY are trying to say that there's no way they could have done something to the transmission during the repair. I called a transmission shop I had used in the past, told them about the intake manifold repair, and asked them if anything could have gone wrong in that process to affect the transmission. Of course, he couldn't tell me for sure without seeing the car, but he told me that yes- it's possible they could have pinched a wire, or done something to the intake temperature sensor that could be messing the car up now. He also advised me not to drive it in its current state- to get a tow truck.

So, is Pep Boys lying to me? Is it possible to mess up something related to the transmission during an intake manifold removal? They say "no, " and the transmission shop says, "yes." Who's right?

Oh, and the beauty of it all? The car's still leaking water. I have a giant puddle under my car as we speak. Pep Boys didn't even give me what I paid for, AND broke my car on top of it. Please help!