Responses absolutely out of order...
"2) Why didn’t removing the excess through the custodian correct the issue?"
There are two types of excess contributions: "short-term excess" and "long-term excess". Unfortunately, the IRS calls them all the same thing. But the solutions to each is quire different.
Short-term excess is excess in the current year. You must withdraw this by the due date of the current return. If so, then the excess is "cured".
But once the due date has passed without the excess being withdrawn, then the short-term excess is converted to a long-term excess.
To cure the long-term excess, you have to either:
1. In a future year when you have HDHP coverage, you reduce your other HSA contributions so that the long-term excess that is carried over plus any current year HSA contributions is less than or equal to the current annual HSA contribution limit. Since the long-term excess carryover is treated as a personal HSA contribution (line 2 on your 8889), if there is room for it under the current year limit, the long-term carryover will be used up, and done with. OR
2. Make an HSA distribution and enter the 1099-SA, showing that an amount equal to the long-term excess was not made for qualified medial expenses. This amount will be added to Other Income and penalized 20%, but your long-term excess will disappear.
"1) If I don’t file the extension and correct the previous returns, will I be taxed the 6% penalty forever?"
If you go under HDHP coverage in a future year AND reduce your annual HSA contributions to match #1 immediately above, that would work. But it means that you would reduce your cash contributions to the HSA for one year...just don't be surprised.
"3) If we contribute about $2,000 less than the family limit for 2023, would that resolve the issue?"
Yes, but haven't you already made your contributions for 2023?
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