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A coil that is on the way out will make this happen, also here are afew other things. I just copied and pasted so if you already did some of it, disregard .
Something else that is not mentioned in here is sticky or clogged injectors.
Fuel pump insufficient fuel pressure, amount of flow
Fuel line clogging, blockage, leakage
Fuel filter clogging
Fuel pressure regulator stuck open
EGR system malfunction*1
Ignition coil wire open, leakage
Ignition control module malfunction
MAP sensor range/performance, poor response*4
Valves carbon deposit
IAC valve malfunction*4
VTEC system malfunction*2
Fuel does not meet Owner's Manual spec., lack of fuel
*1: D16Y5 engine
*2: D16Y5, D16Y8, B16A2 engine
*3: '97 models
*4: '96 models
*5: '98 - 00 models
I found this in a tech line Honda service news article
Here.s something from our .strange but true. file:
On .96.00 Civics, .97.00 CR-Vs, and .96.97 del
Sols, if the MIL comes on intermittently and
misfire DTCs are set, without an engine
performance problem, inspect the alternator drive
belt. If the drive belt isn.t a Honda drive belt,
remove or replace the drive belt, and retest.
Tech Line has had several cases where the
alternator drive belt caused intermittent misfire
DTCs that couldbe resolved only by replacing the
drive belt. The root cause of this problem is
related to the quality control of the belt.