You are going in the right direction, joining a good summer travel team (assuming you will get decent play time and instruction) and working on strength training. Do not allow the HS program scenario to be an excuse. You can overcome it and still enjoy playing HS ball. As you are discovering, you can work on strength/speed/agility on your own, including during HS season. You can also work on skill development - find a decent instructor and then put the learning to practice when you take reps at your HS practices. And since you are a three year starter, I would be willing to bet there is at least one coach willing to give you extra reps before or after practice. This goes for any aspiring college player - you have to make it happen. It won't be up to coaches, instructors or parents.
No need to panic with timing. Many D3's and NAIA's do a lot of recruiting senior season. And, BTW, the JC to NAIA is a fairly common path for many. But you need to take charge and get after it. That said, it would be a shame if you went fully into "prepare for college ball" mode and forgot to enjoy your HS team, even if they are not very good. College ball may or may not work out. Even if it does, it is a different animal and a lot more work than HS ball. Be sure to enjoy your HS experience. Be a great teammate and be a part of making your HS program better. I guarantee if you got several of your HS teammates on board with working out and playing additional ball outside of the HS season, you will make an impact with the HS team. That would be something you will always be proud of.