Elective deferrals to a 401(k) are to be excluded from Form W-2 box 1, but not from boxes 3 (up to the SS wage base) and 5.
If you correct what you report in box 1 of the W-2, I believe that you must also correct line 2 of your Forms 941.
I'm curious, though, how you could get line 2 of Form 941 (and box 1 of the W-2) wrong if you were properly withholding elective deferrals from each paycheck and depositing them into the 401(k) within the proper timeframe. (The Department of Labor requires that elective deferrals from each paycheck be deposited no later than the 15th business day of the month following the pay date.)
