That looks like an excess annual addition. I come up with an excess of $2,852 plus earnings on same, after a few assumptions----
Somehow you can say the first $1,000 removed is the deductible 'employer' contribution. Then you'd need $1,852 more from the Roth deferrals, plus earnings on both of the preceding. The earnings is taxable income for the year 2013.
Calculation based on $17,486 net income from self employment, less .0765 EMPLOYER share of 2012 SE tax ($1338.)=$16,148. No need to subtract the $1,000 if can distribute it.
See Rev. Proc. 2013-12 table of Contents for how to self correct a section 415(c) excess. They might say you have to take employee deferrals first, in which case the 415 limit on annual additions is $17,486 less 1338 less 1,000, or $15,148. In this latter scenario you still keep the 1,000 deductible part, but you remove 1,000 more than when using plan 1, plus earnings.
There's also a rule not often used, 'mistake of fact,' which lets you take money out of a plan once it's in the plan. Overestimating earnings can be a mistake of fact. Can't remember the time frame during which you must remove the funds. Check your full plan document.
I don't see calling the situation 'excess deferral' because you're ok there after including catchup allo
wance. Similarly it's not an excess contributionl, which refers to the nondiscrimination test. So you should not refer to guidance regarding those types of excesses.