I'd replace it, and to do that on your engine requires the left crankcase cover gasket as well since the clutch rod seal is behind the cover with the alternator stator in it. Once a seal has been pressed into the crankcase, it often takes a little bit of the rubber 'skin' off the outside (unless it was replaced during a bottom end overhaul, in which case it's put in position while the case halves are apart). That would mean the seal might not fit as tightly in the crankcase as it did when first installed, so it might come out again more easily.
As I've mentioned before, you can run a little overfull on the oil level safely (typically a half-pint or so in your situation), but you do want to make sure the breather tube is free of any kinked or restricted areas caused by passing through frame areas where it gets a bit squashed or compressed, or worse yet a mud dauber nest in the bottom of the tube where the pressure and vapors are supposed to exit under the bike.
