Let's take these one at a time:

"The bulk of his income is 1099 made out to the LLC."

He needs to issue a W9 to these companies, or a corporate letter, explaining the new FEIN and the new corporation. He also should have done this with, for example, Bank accounts, filing as an Employer, and insurance.

"However he received some w-2's made out to him personally with his ss#."

Then he is an employee of these companies. He also is supposed to be an employee of his S Corp, and supposed to have gotten a W-2 from that firm.

"Can you confirm the w-2's go on his 1040 and not on the S-Corp?"

W-2 = Employee relationship.

S Corps are not employees; they are the Employer of a person that works for them.