So how do we make them harmonize? It appears we have two opinions.
We may understand the Amendment to say that,
The people being necessary for the security of a free state, the right of the people to keep and bear arms shall no be infringed?
or do we understand it to mean,
A well regulated militia being necessary for the security of a free state, the right of the well regulated militia to keep and bear arms shall not be infringed.
The Amendment declares that a well regulated militia is necessary. The right to keep and bear is merely the means to that end. Thus, we must comply with the rules and sacrifice the means to the end.
I don't like it that the lawmakers viewed the right to bear arms as merely the means to an end. I don't like it that the lawmakers didn't clearly acknowledge a right to have weapons for self defense. But, we must respect the words of the lawmakers and the rules of construction, even if we don't like the outcome.