To add. Filling to the top of the sight glass is a little bit over filled. With the bike vertical, you want it to be around the middle. This isn't likely causing your issue, but it can potentially lead to more oil than normal coming out of the breather hose into your air box.
While my gear indicator never wen't dead, I randomly get the same downshift issue you do, where it feels like there is nothing there between the gears. If I take my foot away from the shifter for a second, or even just let out the clutch a tad, it comes back. Mine doesn't happen in any particular gear though, nor does it happen very often. Just kind of like a weird false neutral.
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