It is easier to simply replace all blown fuses than to figure out which is which. Be sure to replace them with ones ofthe same rating.

Ignition coils can get damaged. My coil was hit while pulling the engine and the car refused to run properly after that. I found the problem only by accident as the coil looked ok but was not.

You mentioned shorting out the battery lead immediately before the problem began. It made big impressive sparks and made you feel guilty but I'd not expect that to do much but burn up the nut and bolt you contacted. If the starter cranks the engine, the connection to the battery is good enough to run the engine. You should have indicator lights coming on when the ignition switch is on before the engine starts. The place you shorted has a smaller wire up to the ignition switch. If that wire is destroyed, everything comes to a stop. If it is damaged but still works a little, then running problems can happen. If the headlights still work well, it is probably ok as it feeds them also. Expect the lights to dim when the starter motor is cranking, that is normal.