When you replaced your plug wires, did you install them one by one and in the exact same spot on the distributor as the ones you took off? It sounds like your firing order (the order each cylinder fires in as directed by the distributor) is off. See the diagram I attached to this and make sure your wires match it. The numbers correspond to the cylinder number. For this part you'll need a timing light which you can get at any auto parts store. Drive your car a good 15-20 min to get it at full operating temperature. Next, loosen the bolt holding the distributor in place and unplug the spout connector (the gray fuse looking thing on the distributor wire its about half way down the distributor, its a small cluster of electrical wires). Connect the timing light + and - to the battery then clip the last wire onto the #1 spark plug wire. Start your motor, aim the light down at the crankshaft pulley and carefully rotate your distributor until it's at 12 degrees (that's the timing advance). Turn off your motor, tighten down the distributor bolt and start your engine again to make sure the timing mark is the same and you didn't bump it off when tightening the bolt. Motor off again, disconnect the timing light and plug the distributor spout back into the distributor's electrical wiring and go for a drive. If your engine feels a little off, do the same thing again and try advancing the timing a little more (rotating the distributor clockwise) to 14. Play with it until you get the smoothest performance from your engine. This should also get rid of the "Check Engine" issue. Your engine is either misfiring or the knock sensor is throwing the check engine light because the timing is off and its running rough.
1984 Mustang 331 stroker
1990 Mustang 5.0L convertible