Thanks for the replies. I thought it would be useful to let everyone know what eventually happened.
I had the shop adjust the valves. When I picked up the car, the engine ran fine, but the shop advised me that if there had been valve damage, that the performance would deteriorate over time, and that the head would need to be rebuilt. They quoted me something like $1400 for the head rebuild.
The engine ran well for about a month, but then started to run rough again. I did more digging and found a copy of a technical service bulletin regarding valve problems on my vehicle. I went to the Honda dealer in Tracy, CA and spoke with the service manager. I explained the problem and showed him the TSB. He had a mechanic look at the engine. The mechanic reported that the valves had been misadjusted - the intake valves were too loose, and the exhaust valves were too tight (or vice versa - I don't remember). He recommended that the valves be readjusted. The service manager also contacted Honda Corp. and they agreed to cover the cost of any further repairs, should they be necessary.
I had them adjust the valves. The engine has been running great since then and is now at 156,000 miles with no problems.
This is one time where the dealer's service department proved better and cost me less than the independent shop. Kudos to Honda of Tracy, CA!