Schedule C filer paying himself on a W-2

You don't have salary as sole proprietor, so you can't deduct it. Did he also file 940- 941's 

I think this question comes up here every year or so.  It's not right, but it's a solution for some small business owners who have trouble keeping up with quarterly payments.  Three weeks away from an extended due date, I would deduct it as wages and tell him not to do it again.  Either take a monthly draw at the same time he makes a monthly ES payment; or set up an LLC taxed as an S corporation.  

Any retirement plan contributions involved?

There is no wage deduction as an Expense. It doesn't reduce the Schedule C business income. It reduces the bank. He took his own money, in other words.

Using this as a strategy for paying in as withholding instead of estimated income tax is not the best way to be forced to make your payments. You also have the issue of the employer's share of payroll taxes paid, since that "employer" isn't entitled to payroll tax deduction as expense on the amounts.

Seems like everyone is getting off topic. As stated earlier you cannot deduct owner's salary on schedule C if you want to follow IRS  instructions. If you don't want to follow their instructions that is up to you.