Ugh that's horrible sorry to hear that bud...$3000 to diagnose is robbery, sounds to me they're buying spare parts to try on your dime.
When you heard the zap the car kept running? And when it started again did it use the IMA or 12V starter?
Any aftermarket stuff like audio equipment? Check all the fuses too (but don't replace if you see a burnt one yet)
If you heard a zap and saw smoke my guess is a shorted wire, burnt circuit/module or even a bad battery cell.
Under hood battery at this point is probably dead since charging system is not working . You will need to replace that battery and put the car on a charger for trouble shooting. You may want to find a different shop to work on it. It seems they ordered everything without actually troubleshooting it, getting codes and following the troubleshooting processes from the Factory Service Manual.
There are two ways to troubleshoot: One is to carefully read codes, follow processes and narrow down to the one failed part. The other is just throw parts at it randomly. The second is what this dealer is doing. Find a more knowledgeable dealer who is very familiar with CR-Zs and is ASE certified. Talk to the service manager, if you keep it at the same dealership and ask if they can put their most knowledgeable person on it who knows CR-Zs specifically. Ask if their dealership is familiar with CR-Zs and if they are not can they recommend another shop that is, whether that shop is a Honda dealer or independent specialist.
I hope when all the right processes are followed you will be able to put your CR-Z back on the road.
But that is not a long term solution. You have no IMA and eventually it will kill l the under hood battery( if it hasn't already) and your jump starter but at least you can drive it to a shop. So at this point you do not know if it is the IMA motor or the battery or something else. I hope you can find someone to diagnose it correctly and you can replace what failed.
Any possibility there is any warranty on any part of your IMA?