Also, plug wires, timing. If you're not getting an ECU error code to help you pinpoint the problem, proceed with ignition/running problems by going back to basics. Check components systematically and do not replace on the basis of a guess.
My '89 Si is extremely sensitive to air in the coolant system. It won't start if the air hasn't been bled out. I don't know if this is an issue with later Preludes. If so, and iif you are indeed not getting spark, then this doesn't apply. Of course, if you're getting no spark, you also won't be able to check your timing.