Happens especially on cold starts. Belt and water pump just changed.....immediate engine problem.
Rpm irregularities, vibration and missing after t. belt and water pump change.?? on 1998 Honda CR-V
Are you 100% sure the timing belt has been aligned correctly? Did you do the job or a shop?
Recheck the timing marks, low intake manifold vacuum due to mis-aligned timing belt or a vacuum leak will cause these problems. Valve adjustment is important and often over looked on this engine. Check the coolant level if it is low the idle speed will fluctuate wildly.