Nothing else stood out to me regarding your configuration settings. However after looking at your images closer I can tell you that you have a Mini Gerbil not the “SuperGerbil” as you thought. I also notice you have 2 different A4988 stepper drivers installed which I’d bet are not original with the board. Have you adjusted the current on the stepper drivers? If not you might look on Awesome Tech forum and do that procedure. If not set correctly that could play a role in missed steps as well.
ETA: You might consider remounting the board as well, as fastening it with a plastic strap on top the original board could cause shorts. The Mini Gerbil came with an acrylic enclosure which you can get the drawings for on the Awesome Tech forum.