Should my poor subie be totaled?

I’m mot sure why properly done repairs would lower your trade-in that much, but still, let’s assume you will get $12K trade where you expected $14K.
Insurance will not cover this, unless you sue them and maybe get something back in a loss of value, but it is very likely you will get back less and will end up with legal fees exceeding this on your hands.

$1K lost by asking for new/OEM parts to be used?
Tough luck, but it is what it is.
Some insurances have the option to pay more in premium so you can require them to cover new/OEM parts, I assume you did not think about this aspect before, so next time shopping for insurance you might consider this.

Although I’m not always agreeing to what @VOLVO_V70 says, but here I’m 100% with him: you’ve got into a situation where you can not be 100% compensated for everything you might want to be compensated for… stuff just happens… worry less and see what you can do from what you have on your hands while keeping your sanity

You don’t have to be unreasonable when reviewing the repairs, but you also don’t have to accept anything repaired poorly. If anything isn’t right, don’t accept the car. If you really don’t want the car after it is repaired, then sell it.