Are you talking about the main harness inside the engine cover, PN 32100-ZY2-010, or the harness from the engine to the console and key switch? Or do you know?
Normally, a short will occur in the latter, and it is rather easy to replace. You can order directly from Honda Marine.
The motor is likely worth far more than $500 if it was running well before the short - like ten times that much.
Even if there is a short in the main internal harness, you may be able to find a replacement if you search e-bay and/or contact Honda shops.
Check the fuse box and make sure that all the fuses are good. Don't just look at them, use an ohm tester on each one.
If push comes to shove, do a detailed inspection of the wiring, paying special attention to all connectors, making sure that the connecting pins are not corroded or broken. Pay very close attention to the big connectors going into the ECU. Look for any signs of external burns in the wire covers. As a final resort, get a complete wiring diagram and a good continuity tester and start testing wires.
That motor is very likely worth saving.