Easiest thing to check is fuel pressure. If the needle doesn't budge at all when it starts doing it, you can rule out everything fuel related. You may need a special banjo adapter to place the gauge inline with the fuel filter, I'm not sure if Honda switched to a standard test valve by '99 or not.
Next is the airflow sensor, something you can check by looking at it's output real time with a scanner. Additionally, looking at fuel trims will show signs of any other air problems like vacuum leaks, bad O2 sensors, bad airflow sensor, etc. Closely related is throttle position sensor; same thing as the airflow sensor, you can check it's output range easily with a scanner or even a volt meter. A scope or analog meter would be better for catching and holding fast glitches.
Last is spark; a good spark should be able to gap half an inch with an intense thick orange-blue color. If it's individual coils, you would need more than one of them to be acting up at the same time for it to die; highly unlikely. You can tell a lot about all the components of the ignition system on an ignition scope. This is the hardest thing to check on your own, since you can get a decent spark with a screwdriver but still have problems you can't really see without a scope; most people and most parts places are not going to have a scope.
If it's sputtering badly that means all cylinders are affected equally. Thinking about things that are global to the engine helps eliminate a lot of things like individual coil packs, individual injectors, etc.
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