It depends on what numbers are on your paystubs.
For example, if you think of your W-2, the code W amount in box 12 are the HSA contributions that go through your employer (whether employer contributions or your by payroll deduction). This code W amount is removed from Wages in boxes 1, 3, and 5 on your W-2 when it is printed.
So when you say that you removed your HSA contribution from your gross pay, I hesitate: is this really gross pay, or is this the Wages, which have already had the code W amount removed?
Ditto for the 401(k) contribution (code D in box 12). Dittoditto for health care premiums (code DD in box 12).
So double check that, because I don't want you to subtract things out twice.
Now, look at lines 1a to 11 on form 1040, and you will see ALL the factors in calculating your AGI. For many employees without investments, your W-2 may be your only income.
It is normal to be unable to calculate the AGI from pay stubs - it's not just you.
Just confirm what your pay stubs are telling you, and then keep doing what you are doing...and don't let it worry you that your W-2 and your 2023 1040 and your paystubs all appear to be different.
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