in todays brokerage world, you get the stock transferred, and you issue a sales order, TD does that the same day or at most the next, the difference in fluctuation is minimal, I see no reason to hassle with it.. Now if you were keeping the stock and selling it years later that is a different thing

So when you get the sales amount, that is the amount you use for the donation.  yes on a sales receipt/donor receipt.  When you do that the funds sit in undeposited funds, then use make deposits and put the money in the QB bank account you actually put it 

and in fact do it this way, lets say you get

$5,634.24 from the sale, use make deposits, check off that amount from the sales receipt and on the next line in other deposits section at the bottom select the fee expense account and enter a -$2.00

the deposit will net to $5,5632.24