So in other words, I might simply need to open the aperture a bit more
Well, yes… I guess the only way to really test that theory is to practice. Get a small non-moving object, set your camera on a tripod so it can’t move between shots, and try different aperture combinations. Try to get a good focus, then change your aperture and blow it up to 100% in Lightroom to compare. (Select the photos you want to compare in Lightroom, then hit the “C” key to compare…)