"my W-2 at the end of the year will not reflect my personal contributions"
That's improper. The deposits must be made by the S corp, elective deferrals must be reported with code D in box 12 of your W-2 and the amount reported in box 1 of your W-2 must be reduced by the amount of your elective deferrals. With respect to retirement contributions you are not self-employed, you are an employee of the S corp. There is no legal way to deduct these contributions on your individual tax return.
I'm not sure how you fix this substantial error made by your S corp and it's not clear whether or not you've disqualified your 401(k), so seek professional guidance.
