if I were you, and I'm not, I would not be borrowing money from anywhere, including my retirement $$, to pay down the loan so you can close. Shortsales are done ALL the time, and if its your homestead any difference is typically written off by the lenders with no tax consequence to you, although you will take a hit on your credit score.
I am a realtor for 30 years and am now in the worst "underwater" market in the country: Miami, FL.
So, unless you can easily afford the $20-$30-$40k hit it will likely end up costing you to sell the "right" way, or if excellent credit is absolutely necessary to you, I would rather take the hit to my credit and walk away.
Hire a good realtor with shortsale experience and let them handle the details, or if you prefer to spend a little extra, hire an attorney that specializes in mortgage loan negotiations, though that might be overkill, at least at this point.
Good luck with it