Another thing that can happen with the small Honda twins is that they will run very well on one cylinder at times. They are nicely balanced engines and can seem "normal" when, in fact, one cylinder isn't firing.
A simple test helps identify this condition:
Remove both spark plug wire caps and apply a very slight "smear" of dielectric (tune up) grease inside the lip of the cap. Reinstall plug wires. They will now be very easy to remove and put back for the test.
Start the engine.
Using plug wire pliers,... a thick, DRY glove.... or a doubled up DRY shop towel or rag, pull the top plug wire quickly away from the spark plug. Note the change this makes in the way the engine runs. Reinstall wire.
Next remove the bottom wire and note changes in engine performance.
If the engine changes equally with each cylinder dropped out...even if it sputters and dies in both instances, then the cylinders are each contributing equally.
If the engine runs radically different ie: dies when one is unplugged and stays running when the other is unplugged...then the cylinder that causes the most change when unplugged is the STRONGEST cylinder. The cylinder that causes the least change in engine cadence is the WEAKEST one and should be further investigated.
WARNING! Don't attempt doing this if you have a heart condition or wear a pacemaker as there is the possibility of electrical shock.
It's just another thing that you can try if you think it necessary.
Good luck.