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1) W2 - Box 1:  is it for Gross income or Taxable income?  Neither  ... it is net of pre tax items like retirement or health insurance listed in box 12.
 
2) W2-Box 3, 5, and 16:  are they for Gross income or Taxable income? Will there are the same number for these boxes?   Neither ... it is either the gross income  or  net of certain pre tax items not subject to SS/Medicare taxes.
 
3) For box 12 code b: I have 401 K. If I contribute the total of $3,000 and my company match me to a total of $2,000. Would the box 12b is the sum up of my 401K contribution and my company 401k match?  Box 12 code D will include the amount contributed to the 401K by both you only.  Read the rules here : https://www.irs.gov/instructions/iw2w3