Proceed with all three next steps, no need to check back in between:
Routing: Investigate why the point-to-point router fails on simple nets before defaulting to a full autorouter pass — check whether the current DRC ruleset (clearance/trace width) or the leftover RP2040 footprint geometry is blocking it. Route USB D+/D− (J41) and power/GND nets manually first since those need controlled clearance, then autoroute the rest with neckdowns enabled where needed.
RP2040 footprint: Replace the workaround with a correct QFN-56 exposed-pad footprint with a valid GND thermal pad. Keep all existing pin/net assignments as documented — do not renumber or reassign any nets.
Re-run DRC after both fixes and report final error/warning count.
Enclosure cutouts stay on my end with the measurement photos and calipers — no action needed from you there.