"On my W2 under gross pay, there is a field that states "Less Cafe 125 HSA (W-Box 12)" for $3000. However, my W2 box 12 code W shows my total HSA contribution to be $3499. There is a $499 difference. "
This field - "a field that states "Less Cafe 125 HSA (W-Box 12)" for $3000" - is not on a standard IRS form, so it depends on what your employer (or their payroll processor) intended it to mean.
The code W amount is the sum of what your employer contributed to your HSA PLUS whatever you contributed through payroll deduction. The code W amount should be removed from Wages in boxes 1, 3, and 5 before the W-2 is printed. There is no way you can tell this from looking at the W-2 form itself - you have to ask your employer if they did this.
So my concern is this - did your employer remove $3,000 or $3,499? What is the employer's explanation for the difference?
"In W2 box 12, there is a code C for $166.44. Is this amount already deducted from my W2 box 1 wages? Is this amount subjected to income, social security and medicare tax?"
No, this amount should have been added to Wages in boxes 1, 3, and 5. It's for group life insurance over $50,000 (the employer can't deduct premiums for larger life insurance amount than this, so the larger premiums are paid by you).
Please read "Group-term life insurance" on page 10 in the W-2 Instructions.
"Box 12 shows my RSU vested in 2020. Is this amount already included in W2 box 1, 3 and 5?"
What code was this? Code V? Please see the Code V description on page 20 in the same W-2 instructions above.
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