Assuming that the '98 OBD module diagnosed misfires like my 2001 did, there should be a code for an actual misfire. On one of my tune ups, I didn't have one of the spark plug wires on the plug completely, and when I started it up the first time, it ran rough and threw the cylinder # misfire code. Made it pretty easy to find the culprit.
Running rough, though, might not be a misfire. Could be a bad O2 sensor which should throw a code, the breather filter assy not on the TB tight (code on that, too, and you can hear the air sucking in), bad catcon (code there, too). I'm sure there are plenty more causes, and I don't know if the ones I've listed would cause the running rough all the time or only at lower RPMs like the owner said.
I would only worry about the plenum gasket if it loses a lot of oil. I never replaced mine, and I probably could have. It lost oil its whole life from 1/2 quart brand new to 1 1/2 quarts now over the 3k mile oil change interval. It's burning oil now, though. What bugged me more about that whole thing was that Dodge's idea of fixing it was the death flash that only ******** the timing and robbed HP.