While digging into your transmission issues, don't loose sight of your clutch problem. From your description, I expect you still were not getting full release of the plates when squeezing the clutch lever. You have to wonder if one problem led to the next problem...
Did you check your clutch pushrod travel with a dial indicator to know for certain you obtained the proper movement (minimum of .065 pushrod travel) when squeezing the clutch lever? If you had sufficient pushrod travel, but still had clutch drag, I'd inspect the clutch disc's and spacers for flatness. And, be certain you've not overfilled the primary lubricant. I've found following the MOCO service manual specification for primary lubricant volume can result in clutch drag. I fill my primary with no more than 34/35 oz. of lubricant.