If I were in your spot, I would first go with sand (pool filter sand preferably for ease and low cost) not because gravel will hurt the fish but just to maximize the experience of watching fish doing what they do best. Swapping substate can be a pain but it's something I have no regrets doing.
Then I'd focus the aquarium around the Geophagus since they'll need at least the entire footprint out of your 90g, with the footnote a 6' tank may be required at some point to keep the peace. Mostly because both Geo species are harem breeders and the males will be rough on the ladies, and potentially each other if you end up with a male of each species, who will need space to escape. Again I haven't kept Geo personally so hopefully someone with more experience will chime in, but I want to say the angelfish may be a good tankmate for them. My angelfish are busy-bodies but they typically hang out around the top/middle of their tanks, which would leave the bottom of the tank for the Geo action.
The tetras and Ancistrus should be fine, and I don't know enough about Headstanders to make a suggestion for or against them.
The others could end up working out in the 90g but it might be a good idea to set that 55g up as a backup plan for the Acara, Rainbow, and especially the Pictus.
Alternatively you could get another longer aquarium, which is usually my solution to fish disagreements but I only have my dog to answer to so that may not be a viable choice for everyone 😂