Shares of stock as QCD, do I just do the math?

Wow; is this what happened:

There is no reason to send the shares as QCD, because the growth would not have been taxable to your client as gain, and there is no tax reason to do this as shares. Instead, as RMD, the entire amount is taxable income, so she could have had the shares sold and just sent the proceeds of the RMD to the church.

There also isn't any math to do, because there is no process for excluded gain on something that was in a deferred account and would be treated as income, not gain. You are not handling an Appreciated Asset.

You send shares when you want to shelter yourself from the Gain on appreciated stock price.

Yes, you do the math, shares times current share price.  You do not need to worry about the basis or anything.  The value of the shares was included in the 1099-R so you need to adjust the taxable amount for the QCD. While it might have been easier to sell the shares in the IRA and just distribute cash, there could have been a situation where in kind distribution made sense.  Maybe it was a thinly traded stock and a sale could have moved the market.

I think it was the client who was thinking way too much.  Outside the IRA, a gift of appreciated stock is better than selling and then giving cash.  From the IRA, just sell the stock and give cash -- don't put the burden of making the sale, on the church.