You are one lucky guy in 110 crores population to have a Shogun with a virgin engine and you are wondering what to do?
Dude, I would suggest to keep the Shogun as a weekend bike. You cannot afford to stress it too much. Spares are becoming scarce day by day. For daily commute just go for any regular 4-stroke ones that you feel comfortable with.
Whatever work is needed on the Shogun, plan it in phases and accomplish. That way you do not have to spend too much in one shot. Just take your time with it. But keep it good.