Ugh. 

I vote no 1040X, because "RMD plus QCD" and "no RMD" both result in the same answer of no taxable income, and the IRS doesn't want a 1040X for no change in taxable income or tax liability.

5329 can 100% be filed free-standing. It goes on paper.

As a practical matter, my mom's second year doing QCDs, she had the custodian mail the check to her and she sent it on to the charity with a note of explanation. And she does all her QCDs in January - if the check doesn't clear, it gets redeposited in the same year and that charity comes off her list. QCDs are a great idea in theory, but they are a big hassle.