If I need to issue a 1099-MISC to an LLC and the name of the LLC is ABC Enterprises LLC and is primarily owned by John Doe does the 1099-MISC go to John Doe or ABC Enterprises LLC?

If the LLC has provided an tax ID number, send it to the LLC.

If John Doe has provided his SSN, then send it to John Doe.

In other words, send it to the address on the W-9, using the number provided on the W-9.