99 f150 4.2 idles rough
 

My uncle just brought his 99 2wd 4.2 over last weekend and asked me to put a new transmission in it. I swapped it out with a good used one. However now there seems to be a problem with the engine. It is running very rough at low idle, seems to smooth out as you get up to 2k rpm. Using my $200 scanner it throws an egr pressure switch and #4 misfire code. I have replaced the dpfe, egr, tps and coils this week. I have not changed the plugs and wires yet because the parts cannon is running out of ammo. Lol. Do any of you think some of the wires on the transmission could have done this? I didn't get to drive the truck before I did the tranny, so this could have been a pre existing issue. Any ideas of leads anyone has would be greatly appreciated. I'm running out of ideas

Thanks

Load up some plugs and wires into the parts cannon.

Also check the connections for the front O2's, could have been knocked loose with the tranny change. I know it isn't an O2 code but it helps to check everything.

If the motor was lowered in the back to do the tranny it could have damaged the IMRC against the firewall.

That's my 2 guesses. Good luck.