Well, that's kind of a shame, because now you face what can be a daunting, tedious, prolonged, and frustrating task.My ecu is perfect NOW WHAT?
If the bike was mine, I'd work on finding the short circuit that is taking out the main fuse. Start with a rigorous inspection of all the wiring. Since you say the 30A fuse gets taken out but the other fuses are fine, your short is probably electrically between the + terminal and the fuses, so start by inspecting that wiring. Look for burns, melted connectors, bare insulation, etc.
If you can't find it, you can disconnect the chassis ground, disconnect the ECU plugs -- no sense exposing it to any more electrical insults, since it seems to be just fine now -- pull all the smaller fuses (this is a good time to use your meter to confirm they are all intact), replace the 30A fuse if it is blown, reconnect the chassis ground, and check the main fuse. If it is blown again, you'll have isolated the circuits that could be shorted to those between the 30A fuse and the fuse box. Consult your schematics in your shop manual for the possibilities. (The charging system isn't a bad bet.) If the main is not blown, replace one fuse at a time, checking the main fuse after each replacement. Eventually, it will blow and you'll at least know what circuit has a short.
What you do after that depends on where the short is. It could be as simple as replacing a chunk of scorched wire, it could be replacing some electrical component, it could be replacing the whole wiring harness.