My son was homeschooled completely from preschool to 12th grade. He is currently a cadet at USMA. I will explain about what we did.
My son had his sights set on WP when he began high school. We have no military background, so we had a big learning curve. We read the USMA website and each year looked as what they were looking for in an applicant. ( We started reading here:
http://www.usma.edu/admissions/SitePages/Pros_Cadets_Middle.aspx)
In his sophomore year he attended a few Academy Days presentations so he knew that he still wanted to pursue WP. We also met a field force rep at one of these events and he helped my son with the CFA test. Academically, he worked hard and began county college classes during the second semester of his sophomore year - so he submitted my transcript and also a transcript from county college.
He was not in JROTC (I don't know if it was an option at our local high school) but he was in a wide variety of other things including two sports - karate (an individual sport) and hockey (a team sport). Both sports were through the Rec Dept (and this was not a drawback on his resume. He was able to be a team captain on this hockey team a few times - so that is how the met the 'Team captain goal" (I put goal in quotes because it's not required but we all know that WP likes to see it on the applications).
My son was not is scouts, but if your son is currently a scout and enjoys it, encourage him to become an Eagle. That would help him fulfill the Leadership requirement. Of course, there are other ways to do this, but scouting is a nice way to do it.
My son only did outside activities that he enjoyed and didn't do anything just to look good for WP. That said, most of the activities he did were the kinds of things that a WP applicant would be doing - lots of sports, leadership activities, service projects and he also worked.
If you have any specific questions, I'd be happy to try and answer them.