Glad you enjoyed my thread - but sorry to hear about your car.
I would absolutely try to keep it if the damage is repairable. I personally try to get wrecked cars totaled out if they're borderline, but with what is essentially bolt-on interior parts, I think if the car is in otherwise good condition, it's worth saving. Some pics. would really help us.
The new cost of those parts are very expensive, but I doubt that you'd be out that much if you decided to replace the parts yourself with the help members here parting out cars, eBay,
http://www.car-part.com, etc.
Sounds like you need shift linkage, a window, and miscelaneous trim parts and peices.
How far off is the insurance company's first offer from the "total it" threshold?
You probably want to figure out how much you would get totaling less the buyback cost vs. that threshold. Since you had comprehensive coverage on the car, I assume you want to continue full coverage - which would be impossible with a salvage title, at least in most states. If you don't care about continuing full insurance coverage, or resale, then you might as well go for the best deal possible... negotiating the heck out of it upward and then buying it back.
Again, post some pics or even email them to me and I'll put them up for you. My email address is in my profile.
Keep us posted!
Heath