Have you done anything else since removing the clutch cover almost 3 weeks ago?
Just a suggestion, you might want to document a complete teardown with pictures on here in the event that someone will spot something that isn't right inside. You're probably going to have to split the cases to get a visual on the shift forks and trans gears.
All we did was put it back together after tightening the shift star. We followed the service manual. Something just seems off. Trying to go there this week and mess with it but was hoping to take some ideas with me to try before deciding to pull the engine and start breaking it all down.