1. In the HSA interview, when you are asked if you had HDHP coverage at any point in the year, answer "no". This is true even if you did have HDHP coverage but had conflicting coverage like an FSA.
2. Shortly after this, TurboTax will tell you that you had excess contributions and offer you the choice to withdraw it. Since you have already done that, just answer Yes, that you will.
3. I don't know what the "quarterly fee" refers to. You need to withdraw the entire excess, without regard to any fees.
4. The 6% "penalty" is actually only on any amounts of the excess that you do not withdraw by the due date of the return; this is carried over to next year - this is what draws the 6% penalty that you see on the 5329 and Schedule 1 (1040). If you could withdraw the penalty, then you would have no 6% penalty. But I guess that you are out of cash in the HSA.
5. That carryover will be applied to your next year return (i.e. tax year 2025). If you have HDHP coverage with no conflicting coverage for 2025 (like that 2025). then the carryover will be applied as a "personal" contribution against your 2025 HSA contribution limit, and used up.
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