Rough running

If the plug wires are in the wrong order, you will have a miss at best. Double check that. As far as the alt gauge, that concerns me because the alternator is regulated through the PCM. Check to make sure the wiring harness to it is tight and not corroded. Also, I recommend that you have the alt checked. Most parts stores will do it for free. PLEASE NOTE: DO NOT BUY AN ALTERNATOR IF THEY SAY IT IS BAD. REMOVE IT FROM THE VEHICLE AND HAVE IT BENCH TESTED OFF THE VEHICLE. Often times people replace a good alt only to find out the PCM is bad and causing the problem. Also, check for vacuum leaks. Make sure the idle control solenoid is working and not allowing the idle to drop too low.