Misfiring, also shaking/wobbling in place

I got a pressure test done and they told me it was my intake manifold gaskets leaking so just this past weekend I replaced them. On top of that I replace two idler pulleys, serpentine belt, throttle body gasket, and my thermostat with a friend who works on cars all the time. I was just driving home from work and when I came to a stop my truck was shaking/wobbling in place. When I started to hit the gas it felt rough. I definitely believe it s misfiring because when we were putting back on my coil packs we might have got cylinder four and six switched up but we were not sure. Also, when we were cleaning the area on top of the heads where the gasket goes under the manifold some small debris would fall into the spark plug sockets but the spark plugs were never taken out so we thought that would not do anything. Also, when I got home I looked under the hood and my thermostat was barely seeping coolant out of the housing. I was not sure if I did not tighten it down all the way or if I did it too much and broke the o-ring, but it is brand new and I highly doubt I tightened it too tight by hand and ratchet. Any ideas on any of this?