[Mr_D]

I have the same problem on a 1998 Regal 3.8L K series engine (not supercharged). It started missing while cold, and 2 days later it does it all the time, only 33K miles on it. I haven't found the problem yet. This info applies to the 1998 3.8L. 1999 should be the same.

Some of this will require special tools and a ScanTool to diagnose.

Are there other DTC's beside "misfire" recorded? DTC is Computer (Diagnostic trouble code).

Inspect vacuum hoses for splits, kinks, or improper routing or connections.

Inspect PCV valve and PCV O-rings.

Inspect throttle body inlet screen or damage or the presence of foreign objects that may alter the air flow through the MAF sensor.

Check Fuel pressure (48-55 psi) if above idle.

Check for excessive water, alcohol, or other fuel contaminents.

Inspect the PCM injector grounds, power grounds, and sensor grounds ensuring they are clean and tight.

Inspect for vacuum leaks in the:
Intake manifold
EGR adapter
EGR Valve
EGR feed pipes
Injector O-rings

Remove and inpect the EGR valve to ensure that the pintle is not sticking partially open. also check for carbon deposits that may interfere with pintle closing.

Check fuel injector operation. Injector leakdown test pulses each injector, one at a time, and measures the change in fuel pressure with engine off. The fuel rail can be charged by turning on the ignition a couple times. Each time ignition is turned on (not started) the fuel pump runs for 2 seconds to prime the system. The fuel pump remains on only if the engine is running and during starter cranking. The fuel rail remains charged for days unless there is a leak.

A 2nd fuel injector test measures injector current draw. Mine were all 12 ohms while off. That is not a complete test but just a baseline and doesn't indicate if they function, just that the coil is intact.

Check Ignition Wires, coils and spark plugs. Check wires for carbon tracking, damaged insulation, or improper routing that could conduct the spark to ground or other wires.

Measure ignition wire resistance, should be below 7K ohm. Mine was 1K ohm. Longer wires will read slightly higher.

Measure ignition coil secondary resistance, spec is 5-8K ohm.
Check for carbon tracking here also.

Check for a damaged accessory drive belt, pulley, or accessory.

Check for lose or broken motor mounts.

Check tranny TCC (torque converter clutch operation). Should appear like a 5th gear above 50mph and generally stay engaged at speed.

Replace ignition control module.

That's it. There are much more details but almost too much to write here. Of course, a worn cam lobe, valve or bent valvetrain component could also cause a problem, but it wouldn't come and go, That would be all the time.
Mr_D.