Smoke,
So, I think you need to find a "guru" in your area....to borrow Goosegg's term. We found a guy in our area who was a former professional pitcher that worked well with all three of my kids. All three of my kids are very, very different from each other and this guy was able to work with them all based on their different abilities and personalities. That took care of the mechanical and developmental part of pitching. They also played positions in high school so we also included hitting mechanics in some of the lessons. Paying a professional to work with my kids was well worth the money...mechanics is everything in pitching.
In conjunction with the pitching instruction, we "rolled our own" and adopted a combination of the Jaeger program and long toss that we followed very closely during the (high school & travel) season. We stuck to the KISS principle of keep it simple stupid. Like the Hoeflins program that Goosegg mentioned, my kids were not lifting weights above their waist. It was all about flexibility and core strength. This carried over into college when my oldest was doing more intense weight workouts below the waist but never above. His college pitching coach was a firm believer in yoga, band work and long toss above the waist.
Good luck!