I seriously doubt that anything is wrong with your transmission, but it is probable that your clutch plates can be sticking. But first, a couple of questions.
When you pull the clutch lever in, does it â€œfeelâ€ the same as it did before you removed the sidecover? Is it softer, or is there more â€œfree playâ€ in the lever than before?
Put the bike in first gear, take it off of the stand, pull the clutch lever all the way in and rock the bike back and forth forcefullyâ€¦does the clutch disengage and allow the wheel to turn? Even with everything working perfectly the wheel will not spin as freely in gear with the clutch pulled as it does when it is in neutral.
If the clutch does not disengage after rocking the bike back and forth with the clutch pulled in, my first thought is that the lifter mechanism is not â€œclockedâ€ properly and may need to be rotated a little more to allow the clutch to completely disengage.
There is no need to start adjusting ANYTHING else to make this work. If there is an excessive amount of free play in the lever, do not adjust the clutch cable to correct it. That will be an indication that the clutch lifer mechanism is not installed correctly.
Where do you live? If you are near the Charlotte area I will be glad to take a look at it for you.
Let me know what you find out.