'98 DOHC 2.4 Miss at Idle

Hello everyone I'm hoping someone can help me. I'm working on my sisters 98 GA with DOHC 2.4 Quad4. It has roughly 228000 miles on it but recently she drove it up on a rack to get new tires put on it and when she came down off of it it had a miss (at least that's when she noticed it). Its just a slight miss ~800 RPM It gets real bad at 1000 RPM then pretty much goes away at about 1200 RPM. We replaced the plugs, it had new plug boots, and tried new coil housing and coil packs, still nothing, I couldn't find any vaccume leaks, I followed the haynes manual to testing the TPS, which indicated it was bad, but replaced it and it didn't help (I think the TPS Check is wrong in the manual). It has new injectors, and Fuel pressure regulator. The one thing I haven't done yet is a compression check (I wonder if it could have developed a head gasket leak that is fouling out a cylinder?) I don't notice any significant amount of steam from the exhaust. So if anyone can throw me a bone I'd greatly appreciate it. Also, Natrually the check engine light came on(it just says "Multiple Cylinder Missfire") and when I try and clear it by removing neg. battery cable for any period of time It comes right back on instantly as soon as you start it like it never cleared. I have no experience with OBDII computers but in my 72 Tuned Port Monte Carlo(86 model Injection(OBDI)) all I have to do is disconnect the battery to clear the codes, does it take something special to clear them on this car? or is there just something that serious wrong with it? So, Once again if anyone can help I'd surely appreciate it.
Thanks,
Justin

The OBDI and OBDII systems are different. The computer will not clear some codes by disconnecting the battery like in the OBDI system. You need a code scanner to clear the code but it sounds like you have an issue that is not going away. As you indicated I would do a compression check just to see what is going on. There is a possibility that you have a dirty injector or possibly a bad ignition module you should be able to tell if anything is going wrong internally by the color of the plugs when you pull them out. A cylinder that is too rich will show a dark wet plug and one that is lean will show a white colored plug. May point you in the right direction.