The phrase "well-regulated" was in common use long before 1789, and remained so for a century thereafter. It referred to the property of something being in proper working order. Something that was well-regulated was calibrated correctly, functioning as expected. Establishing government oversight of the people's arms was not only not the intent in using the phrase in the 2nd amendment, it was precisely to render the government powerless to do so that the founders wrote it.
1812: "The equation of time ... is the adjustment of the difference of time as shown by a well-regulated clock and a true sun dial."