"But what probably threw the monkey wrench in it was that we had a decent bonus that year, so additional was contributed from that separate check, as we never knew what the bonus would be until just before it hit. "
If you were still working, I might suggest to the HR department that they talk to employees about this. because overcontributing can be a hassle, and, as you say, you have no way of planning for it (unless the company policy would be to take no HSA contributions out of bonuses).
Still, this explains why you had an excess in 2023, so no need to amend 2023.
The 5498-SA comes from your HSA custodian. However, it is for your records only because you don't enter any part of it into your tax return.
So it sounds like you can continue with your 2024 return. You can make the choice to delete the 8889 or not...and maybe some day, the IRS will address this situation.
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