Line 1 on Form 1040-X is the adjusted gross income line and because the QBI deduction is taken against taxable income (and not AGI) it should be added to AGI on line 1.
IRS instructions for Form 1040-X provide that line 2 can include not only the standard deduction, but also, the cash charitable contributions. In this regard, the instructions state the following:
"Include on line 2 with your standard deduction amount your charitable deduction, if any, for cash contributions that you are allowed to take with your standard deduction." (underline added)
@baddogg