Next steps
The project still needs a safe net-intent pass before cleanup: resolve the large set of floating pins on
U1,
U2,
U3,
U4,
U5,
U6,
U7, and
J2, then reduce portals/grounds, rename anonymous nets, and manually re-place the layout. I cannot complete the requested full cleanup and compact placement with the current project state because symbol movement / schematic visual reorganization and PCB component re-placement are not directly executable here, and further destructive net cleanup would risk breaking the architecture before those unresolved pins are classified.