Question 1: No. The medical expense deduction is the expenses in excess of 7.5% of Adjusted Gross Income (AGI), which is Form 1040 line 11. AGI includes the long-term capital gains.
Adjustments to income are listed in Part II of Schedule 1, and the total adjustments from Schedule 1 are on Form 1040 line 10. Adjusted Gross Income (line 12) is the total income on line 9 minus the adjustments on line 10.
Question 2: Yes, the standard deduction replaces itemized deductions. Medical expenses and mortgage interest are itemized deductions.
HSA contributions and educator expenses are adjustments, not deductions. They have nothing to do with whether you take itemized deductions or the standard deduction.
A dependent care FSA and 401(k) contributions are not deductions.
If you have dependent care FSA benefits in box 10 of your W-2, that amount is already excluded from the wages on your W-2. If you actually used it for child care (day camp) it will not affect your taxable income.
401(k) contributions shown with code D in box 12 of your W-2 are already excluded from the wages on your W-2, so they are not included in your taxable income.
Question 3: You take your Adjusted Gross Income and deduct the standard deduction (or itemized deductions) to get your taxable income.
Why don't you just start entering your information into TurboTax and see how it works out? If you enter estimated amounts, you can go back and change them later when you have the final amounts. If you use the CD/Download TurboTax software, not TurboTax Online, you will be able to see the details on the forms as you go.
