Sounds like you answered a lot of it yourself. Good deal on it running good now! I would replace the oil seal if your getting oil in the recoil, not that hard to do. Since you had the left cover off i would get a new gasket for that as well to stop any future leaks, also get a new o-ring on the bolt that holds the recoil pulley to the crankshaft.
If the voltages stays up and the battery stays charged your good, if the voltage sags down low again like that then replace your regulator/rectifier. I had a few do this, my 200ES did it last summer also, the battery would run down and always need topping off and when i checked the voltage without the battery connected i only had around 5-6v output. However if you check the AC input to the rectifier/regulator and you see 10-30v AC there depending on engine speed then you can rule out the alternator/stator coil. Its usually just a bad regulator/rectifier unit, but it sounds like your battery was pretty dead also.
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1984 Honda ATC200ES "Big Red"
1982 ATC200E "Hondie"
1988 TRX300FW "Project Quad" Still in progress....