When replacing the countershaft seal, after you pull out the collar and seal, clean up the area with contact cleaner, and you want to use some Yamabond #4 on the end of the collar that rests against the bearing. This will seal the collar from leaking through the splines.
For the oil level, I always pull off the clutch primary cover to drain the trapped oil that doesn't drain out through the drain plug, then I know I'm dry, then add 1500 cc's of 2 stroke transmission oil like Maxima MTL, Belray gearsaver etc. I like 80w for street bikes and use 75w for track bikes.
Team Scream Racing