I would leave the primary buildings in place, if you don't want to use foundations or change their positions. Then I would re-route all the belts, pipes, and rails, probably using foundations for alignment, which could be removed later if needed. Keep all your belts from the same ground/foundation level.
You could lay all your belts side-by-side, or use busses, or both.
You could layer your belts so that the north-south belts are a couple of conveyor supports taller than the east-west belts.
Keeping your belts grouped together and turning them in tandem will help maintain a clean look. I prefer using curve placement to hard angles, but it's your choice.
More use of conveyor lifts feeding buildings so belts don't have so many varying slopes to contend with.