If the client has employees, they NEED to have a W-2, NOT a 1099-MISC.

"The owner didn't have 1099-MISC or W2"

If it is taxed as a corporation and if the owner took out money for personal use, the owner NEEDS to have have been on payroll with a W-2.

"I faxed 2553 with relief request"

What was the "Reasonable Cause" for not filing the 2553 on time?  There must be "reasonable cause" for not filing it on time, such as the owner thought it was already filed.  You can't file it late just because it sounds like a good idea.  So that includes ACTING like a corporation (because they thought it was already filed), such as the client being on payroll with a W-2.

"Can I efile late 2553 attached with first S Corp return now? ... I faxed 2553 with relief request"

If you already filed the 2553, why would you file it again?

Because there are many questionable things going on here, I certainly would not file without the IRS acceptance.  Although there could be more information that you have not told us that could change things, if the 2553 had not already been filed, I don't think I would even try to file a 2553 because it doesn't seem like they qualify.