1999 Ford F-150 engine is backfiring after tuneup

I replaced my upper manifold gasket due to a vacuum leak. I also replaced plugs and wires. Cleaned the throttle body. Well after putting everything back together I cranked the motor. The vehicle runs great in park and neutral. As soon as it is put into drive the motor bogs itself down, idles extremely rough and backfires. I have know idea where to start on looking for the problem. What would cause this to happen after doing the work that was preformed?