Hi and thank you for your question.
I suspect the problem you are experiencing is because of the clutch release mechanism.
First, when you are trying to install the primary cover and it stops about 1/2" away from the cases, do you have any free play in the clutch lever? If not, you will want to collapse the cable adjuster all the way. That entails breaking the lock nut loose at the cable adjuster and screwing the externally threaded portion of the adjuster in as far as it will go into the internally threaded adjuster.
Here is a parts diagram of the cable and lever. If you will look just below the reference #8 you will see the adjuster I am talking about. You want to make it as short as possible which will give you maximum slack in the clutch cable. Just to make sure I am being clear on what I want you to do, after you screw it in, you should not be able to see any threads on the adjuster any more. Just trying to ensure you screw it in as if you were tightening a bolt as opposed to backing it off.
Once you have the adjuster bottomed out as described above, try installing your side cover again and see if it will now go.
Once you get the side cover on, you will want to back that adjuster out so you have about 1/8" free play at the lever perch between the perch and the cable ferrule.
If you have any more questions, feel free to ask.