EIN matches the owner's name on Line 1, so looks like that's okay. I was interpreting instructions literally -- Here's an excerpt from General Form 1099 instructions:

For a single-member LLC (including a foreign LLC with a U.S. owner) that is disregarded as an entity separate from its owner under Regulations section 301.7701-3, enter the owner's name only on the first name line and the LLC's name on the second name line. For the TIN, enter the owner's SSN (or EIN, if applicable). If the LLC is taxed as a corporation, partnership, etc., enter the entity's EIN.

Payor did not enter LLC's name on second name line. If that's not an issue, I won't ask my client to have payor reissue.

I don't believe she has elected S Corp status yet but has done 2021 one-time/single payroll as if she has following her CPA's guidance. New CPA told me (in 10/2021) he would elect S Corp status when he files her taxes for 2021, but unless an exception applies, I didn't think she could do that. I thought she would need to file as LLC/Sch C for 2021 income and then, beginning in 2022, she could elect S Corp status, pay herself reasonable salary, run payroll, etc. to reduce S/E taxes. 

Regarding which box to check, I reviewed it again and agree LLC box should be checked with "S" filled in once that election is made for all future W-9s. 

Thanks.