For the basic stuff in my opinion the best place for self learner is Kenny Weldon

For the punching problem i can imagine two-three things.
First you punch with alot of overhand type of punches without the necesery flexibility
Second the sholder problems are related to the back problems... The herniated disks may force your posture in bad possition or the oder way around...
The third you push the bag too much and this results in overstressing the sholders. Here you don't thing the sport of boxing as a sport. In all sports the ideia is to move fast some kind of inertia. In boxing you try to rotate your body as fast as possible, which leads that the bag is not there to be pushed by you, but just to stop you... In this way of thinking the sholders are there to possiotion your hand to transfer the rotation impuls into the punch and not to create additional power.