Motor swap

We swapped a motor from two 1997 F-150's. The one recieving the motor has a full club cab on it, the other has a short extended cab on it. Both motors are the same size. We had problems putting the motor in because although they are the same, the mounts did not match.

Now that it is all in place the motor does not run right. It has a little steady miss to it that causes it to run rough. Speeding up quickly did not help. Running slow or fast it still skips. Kinda lick going over little speed bumps.

My Mom drives the truck down a dirt road and we want it to be right so she does not get standed. We replaced the spark plugs but it does not help. We have several mechanics fussin over this and I would like to hear from someone who may come up with something that may work.

Thanks