The optimized route found for skulls was: Getting the dagger as starter Doing the Wall Doing the Noose (retrieving Rope) Doing De profundis Trading Rope and Dagger with Fly and Goblet Doing The Twins Doing The Presence of the Scorpion Retrieving the egg

Can be better if you can randomly steal Goblet or Fly.

Done with FS-UAE emulator with basic options but removed disk noise.