This is all very fixable. When I was coaching my peewee league football team, I decided to incorporate the shotgun into our offense too. The problem was that my 11-year-old qb would then continue to drop back an additional 4 or 5 steps backwards after getting the snap. In a desperate attempt to prevent him from doing this, I did what any super football genius coach would do - I put a shock collar on the neck of my quarterback.
Everytime the little tyke had the ball hiked to him from the shotgun position, if he so much had taken an inch backwards, I would immediately "zap" him as punishment for his mistake. After about 5 or 6 "zaps" (including a few accidents where he pissed all over himself), he started finally getting it and would only move up into the pocket when his protection started breaking down. This technique proved so successful that I started incorporating the shotgun into every other play when we were on offense.
And even though we only won 1 game that entire season, I still felt strongly that we could have been a .500 team the following year had it not been for the major lawsuit I was facing by the parents of the quarterback.
Sheesh! You'd think that they would have appreciated the efforts that I had taken to make their son a better player.