This Could Be Quite A Project.
Do Have Comprehensive Insurance Coverage On The Vehicle ?
Have You Confronted The Repair Shop About The Mold Situation ?
This could be a difficult DIY job. If carpet padding got wet and if the padding is natural fiber material then it will possibly need to be replaced, not so much with synthetic materials.
Perhaps a flood damage restoration service company could have a look at it. You can try an auto detailer for suggestions, too.
Unless somebody can pinpoint the source of the mold odor then I'd think the whole interior would need treatment.
You're quite sure the mold isn't in the HVAC system ? Air conditioners like growing mold and spewing bad smells, even when windows weren't left open.