It looks like the only amount you need to exclude from being taxable is the rollover amount. As you go through the followup questions, you'll be asked what you did with the money. Check that you rolled it over to a n eligible plan, as opposed to some other use, and you'll be asked to enter the amount of the rollover. The tax withheld is entered on the 1099-R. That amount is not directly applied to the 1099-R. Rather, it is entered and added to all other withholding on your return and applied to the total tax owed on your return. The cash and the transferred stock are taxable transactions.
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