You'd enter the bargain element already taxed as your client's income as cost basis in the exact same screen you enter the sale.

I'm confused though... "Morgan Stanley shows the taxable compensation... as well as taxes paid (including SE tax). I don't see anything on the W2...

So, is your client an employee or independent contractor?

Is the bargain element showing as taxable compensation or not?

Ask for documents for the grant and vesting as well as the payslips.  The information has to be there.

[Edit: Forget about the part about Sch D.  Thought the OP asked about sale of stocks received from RSU.]