I have a 05 mustang 4.0 five speed and it sounds like it has a miss at idle and jurks and shakes though 3rd and 4th no codes come up and it started after I did a tune up
If you put the plugs in without gapping them, they may be gapped for a different application. I don't know the 4.0 well, but if it has spark plug wires, make sure they aren't damaged or laying on a hot manifold. If it has Coil Packs, make sure they are seated properly and the boots are OK. Like Sparta says, double check your work.