Sounds like the sub-frame is a likely culprit.
You'll need to pull some (mostly plastic) parts to confirm but seems likely, especially in a crash with side cases. Cases will put lateral forces on the sub-frame in a crash which it really isn't designed to take.
I see that they run about $418 on Cheap Cycle Parts - see attached image. I'm guessing this is an install that I'm unlikely to be able to do myself, in the event that it is bent.
Replacing it seems like overkill to me, its not a structural component. Its just there to hold up the rear fender and your rear end. You and two of your beefiest friends can probably wrestle it back into alignment or close to it with cargo straps, come-along or some other contraption without removing it from the bike. Its an opportunity to be creative (and cheap). It won't effect the ride, tire alignment, handling, etc. if its off a little but if you can get it straight enough it should be fine.
I'm still a newbie with tools and motorcycle mechanics.
No time like the present to learn.
Has anyone replaced the sub-frame themselves? I'm curious about how involved of a job it is, i.e. how long it's going to take a mechanic to do it at the shop, i.e how much it's going to cost.
If you can't DIY then your bike is very nearly totaled if you have to pay someone else to do the work. You'd be better off stripping the parts/farkles that you want for your next bike and selling the carcass as a parts bike on ebay/CL if you have to pay someone to do the work. Sorry.
One non-moto tip; you should step away from the bike and not think about it or work on it or make any fix/sell decisions for at least a week. You just had a bad wreck and you need to decompress before you make any decisions. You sound like you still might be a little amped up.