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Did you clean the TB real good? It should be airtight when closed. With that out of the way, did you clean your idle air valve? It's an electrically controlled valve that regulates the amount of air bypassing the throttle body.
Now, let's assume that your ignition system is fine (power stage & coil, wires and plugs good, distributor cap & rotor good, etc.).
If your car has an original fuel pressure regulator, it's time to replace it anyway, so just do it. The fuel pump probably is not original, but if it was replaced around 60-70k miles you may be up for a new fuel pump too. That's just so that you know.
Now, after scaring you out of 150 bucks for FPR and fuel pump, let's check the simple things first. Vacuum leaks. Everything between the intake side of cylinder head and the throttle body must be 100% airtight. That means that you must do the water spray test (and WD40 too) of air-tightness - look in the FAQ. Spray around intake manifold seal, throttle body seal, injector seals
Many of the rubber vacuum hoses (long ones and short couplers) may be leaking to some extent at that age of the car. It will be inexpensive enough to replace them anyway just to get it out of the way.
That should more-or-less summarize what you need to look for.
Note that a new FPR will have a faster response than a 12 year old one, so unless it was the main cause of rough idle, it will probably make the idle rougher. In which case fuel pump and air leaks are to be checked. With a new FPR make sure that the fuel pressure is OK and that it doesn't fluctuate. If it's fluctuating, change the fuel pump (both of them if you have two).
I would look for vacuum leaks first and check ignition and fuel pressure as well. Note that the fuel pressure may be fluctuating due to vacuum leaks and FPR correctly doing its job, so get rid of any vacuum leaks first.
Cheers, Kuba
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