Should the wages reported on W2 be my Gross income or gross minus deductions (which is what mine shows)? Should box 12a be deductions + taxes taken out or not?

It is your gross income MINUS any TAX-EXEMPT fringe benefits.  Some fringe benefits will reduce Box 1 of your W-2, some reduce Boxes 1, 3 and 5 of your W-2, some don't reduce them at all.  It all depends on the type of fringe benefit.

box 1 should reflect any allowable deductions in box 12.  not everything in box 12 is a deduction against taxable wages in box 1.    

your gross wages federal is reduced by the amount of your 401k contribution by the payroll dept. That amount will be listed as a box 12 item.