This is Meaningless: "I already exceeded the SS limit on a different W-2"

Because that requirement is per Employer.

This is an Error on your part, as the Employer: "I must however, write in Medicare withholding of $123.  The  problem is I didn't submit a 941 meaning I didn't pay the $123."

The 941 is for Payroll. Not just because there is or is not something that needs to also be paid in.

"Do I wait for the IRS to bill me for the $123?"

You need to finish all of your payroll paperwork, even if it is This Late. Your 1120S is wrong, too.

You need Professional Help in person.