Yikes! What a nightmare.
Some things come to mind. The alternator's voltage regulator (diode
type) may be fried and allowing the positive to ground. The diodes can
be replaced if necessary. Suggest you temporarily disconnect the wires
to the alternator to see if the massive shorting problem clears, or not.
I'd say the good news is that the engine runs indicating that the ECU
may be OK.
The lack of idle may be due to the idle speed controller not
functioning, either from no power or that it's fried.
Modern cars' electrical systems are very complicated and this won't be
cheap to fix. Each subsystem needs to be isolated and tested - buy
dozens of fuses or an amp meter to check the flows.
Repairs might be covered under your comprehensive insurance policy.