If I contribute $5500 directly to my IRA and $1560 via payroll deduction to a 401k (W2 box 12a code D Retirement plan checked in box 13) do I have excess contributions?

You don't have excess contributions because IRAs and 401ks are two separate things, and you are within the contribution limits for both.

Whether the $5500 traditional IRA is deductible is another story.  If your modified AGI (roughly, your income) was less than certain limits then the entire contribution is deductible. The limits are $61k for an individual return and $98k for a joint return.

See the IRS chart here: IRA deductibility - covered by employer plan

The $1560 401k contribution will be deductible, regardless of income.

edited the $61 to $61k