Training Wheel Hero
Join Date: Jun 2014
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The metal shavings are most likely from the impact of the case breaking. It is unlikely that the top end (pistons/rings/ cylinder head) received enough of an impact to jar any metal loose.
If I were you I would remove the right side cover completely, and let all the oil drain out. Then get a lot of rags and wipe as many surfaces as possible to get more of the contaminants.
For the old silicone on the case mating surfaces use a razor to remove the remnants of silicone. This works better and is not as messy as solvents.
You stated you have a new right side cover. You also must have a new gasket. Do not proceed without one. Also, I like Yamalube gasket sealant, but Honda probably has something similar. Purchase some sealant when you are getting that gasket.
Install the clutch cable into cover at this time per service manual.
Now for the install. Wipe the mating surface of case with alcohol. Also wipe the mating surface of case cover with alcohol. Let dry. Next put a very small bead of sealant around entire case surface, and put a very small bead of sealant around case cover mating surface. Let both dry for 5 minutes. Now install the gasket onto case or cover (whichever is easier) and now install the cover to the case. Torque the bolts per specification. Wipe away excess sealant and allow to cure for 24 hours.
Next, install drain plug. Pour 1 or 2 quarts of oil into bike and then let drain out in order to flush case of any more contaminants. I would use cheap car oil since you are going to drain it anyways, but this is up to you.
Finally, install oil filter and torque drain plug. Fill bike with your favorite 4 stroke oil.
You should be good to go, but if you are still worried about contaminants (which I wouldn't be) then let your bike idle for 5 minutes, and then change the oil and oil filter again.
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