Turbotax is not applying the 401 contribution or 3k cap loss carryover. I see it listed as expenses, but then on the summary page it does not reduce the income

Look at your tax return to see the reductions.    The summary screen in TurboTax will show all of your income before deductions.   

 

Your 401K contributions are not in your Box 1 wages and therefore already removed from Line 1 of Form 1040.   The code D amount from Box 12 of your W-2 is removed from taxable income and not included in your Box 1 total.  

 

You will see your capital gains deducted on Line 7.   Preview Form 1040 in TurboTax Online.

 

Use Forms Mode if you are using the desktop software.