The shift motor might have gotten water inside it. Or the shift motor may be going bad... worn out brushes, bearings etc., causing excessive current draw. Or, the reduction gearset may have a gear with a broken or chipped tooth. Any one of those might smoke the ECM again if not corrected.
While you are checking the shift motor and gears out, take each gear out and wash them in solvent. Inspect them and inspect the supporting bearings in each half of the housing. Make sure none of those bearings are cocked in their bores. If you find that a gear has been rubbing on the housing straighten up those bearings. Then push some quality grease past the shields on each bearing using your finger, packing each with grease. Then coat each gear lightly with grease (coat the gear teeth) and reinstall them, making sure the lower gear is installed on center. You can download a copy of the service manual HERE
to use for reference.
Then move on to testing the shift motor. You can put 12 volts on it on the bench to see if it runs. Reverse the polarity of your 12 volt leads to test it in the opposite direction. It should torque over strongly and rev up immediately in both directions. Let us know how the shift motor tests out before you go out and buy one. We might be able to solve that problem.
If you buy any parts buy genuine OEM Honda only, or you'll be buying them again immediately. DO NOT put ANY china parts on the bike. Those are all garbage dumped here to rob you, destroy your standard of living and destroy the value of your Honda! Have fun!