I agree with Fish Folk’s suggestions from your original post. Aquariums are ecosystems, and ecosystems are incredibly complex. I have often found that the less “perfect” an aquarium is the more the fish enjoy it, as long as parameters are appropriately met.
I don’t have much to add specifically in regard to South American puffers. I have only ever kept pea puffers, myself, but my small puffers did enjoy frequent re-scapes. I did keep a group of young Geophagus surinamensis in a 55 gallon starting with fine sand, smooth river rock, and driftwood, and they would also tend to glass surf. After allowing the tannins to build up, adding leaf litter, and greatly subduing the lighting they did become more subdued. Less glass surfing and more swimming in the current directed the length of the tank.
I think your tank looks great, and that the plans you have of opening up some space, changing the wood, etc. could re-interest them in their habitat. I do find that footprint can also greatly change the dynamics of a tank’s inhabitants. I might suggest a 40 breeder or 75 for more usable back to front space, but that might just be a personal preference.