I had this exact problem, same problem on my ZC.
After it warmed up, it would intermittenly pulse from 750 to 1200 rpms. Almost like I had a set of cams. I tried everything diagnostic and even stumped a couple qualified Honda techs. Replaced and/or substituted a lot of parts, even the ecu. Followed the Helms troubleshooting until there were no other options.
Anyone remember David Moore? He even spent an entire day doing diagnostics with his obd-0 datalogging tool. With it being intermittent, we spent the entire first half of the day not experiencing the problem...but it finally started doing it in the afternoon.
Based on the datalogging, the ecu was getting some freaky o2 sensor input and responding in kind. Like the ecu expects to see a voltage range of, say in generic units, 50-60 but it was seeing like 10-200.
I had already replaced the o2 sensor, checked the wire for breaks, grounds whatever. Replaced the o2 sensor again...still pulsing.
The header I was using put the o2 sensor right in front of the cat. Some people theorize this is a bad lacation for a non heated o2 sensor because the exhaust gas has cooled enough not to be read correctly by the time it reaches that location.
Tried swapping back to the stock header, the problem stopped and I thought I had it solved.
It was back a couple days later...
After all my own efforts....paying for dignostic time with a Honda tech and a private garage, Davids time, all the parts, sensor swaps and electrical troubleshooting...and the fact that the thing burned roughly a quart of oil every 2000 miles I had had it.
This was the final straw in deciding to put a new engine in. Not another used a ZC. One that was freshly rebuilt.
Not what you wanted to hear, I'm sure, but maybe my experience can help somehow.