SOLVED!! At least to my satisfaction. Your mileage may vary, I guess.
I know the errant bubbles don't really take away from the function of the filter, but I really just didn't like seeing them. It could be an issue with knowing they can be "optimized" and mine wasn't. So, I included the steps I took below as well as some pictures for reference.
1. Shorten up the male end of the air stone. I tried this by itself thinking I couldn't shorten the tubing any further so this brought the air stone up a bonus 1/8'
2. Find yourself a takeout sauce cup. the ones they give you extra oil and vinegar in at a sandwich place.
3. Cut the side of the cup and then cut off the rim then cut off the bottom. I then took the curve out of the plastic to make a nice 1/2" clear strip.
4. Take that strip and tuck it between the sponge and the frame.
5. Enjoy
I know you can do the same thing with an extra tube and what not, but I didn't have any parts like that laying around. Hope this helps anyone looking for that "optimized" experience.