2000 Ford Explorer occassional misfire

'00 explorer 4.0 ohv started misfiring cyl 1 after I installed a flowmaster muffler. I thought I could handle it and checked coil, plug, wires, anf uel injectors. Everything looked ok, with exception to the coils, cyl 1 was not putting out enough. So I replaced coil pack and cyl 1 plug with a motorcraft plug. Mechanic thought it may be a pushrod from me revving it. He did a compression test, said cranking it was 90 and then started it was 0. Did a wet test, cyl 1 jumped up. But I dont smoke at all, so I really dont think its rings. He also checked for vaccum leaks. I picked it up from him and surprisingly it runs better, it doesnt misfire as much, yet. However, on occasion is will misfire when I am stops or in a parking lot, etc. But as soon as I drive, maybe 45 seconds it smooths out and stops, even when I come to a stop again. Any help would be appreciated. Thank you