I thank you all for the help. To answer some of your questions: There are no good hitting instructors that I know of locally, so I haven't gone that route. He doesn't want to play any other sports, not sure why (I wish he would, he has the perfect physical attributes to be a great run n'gun QB)
Our plan was long toss 2 times a week plus the switstik/whiffle ball drills in the basement with as much catch and live hitting as weather allows. We also do some Epstein drills as well as some of Mankins stuff. Kind of a hybrid of the 2.
We live in IA (town of 80,000), but baseball takes a back seat to football, so we don't even have year round batting cages, let alone a fall league. The best news is that we are moving to Omaha this time next year, I have already found a hitting instructor, an indoor facility and a fall league, so things are definitely looking up.
I never thought about speed and agility training (GREAT IDEA), he is already quick, but I have never seen a kid that was too quick, that's for sure. Especially since he will have a lot more ground to cover at short next year.
Again thanks, and I look forward to any more advice.