The 1099K is used to report income that will be included somewhere on your return.
In your case, you will be reporting the income as capital gains income. The IRS may indeed expect to see this as Self-Employment income on a Schedule C, but all you need to do is respond by sending the IRS a letter saying the income was included on Schedule D. You can include the accounting of gains and losses on your sales and your other expenses. You can even prepare that accounting now in a manner that you would want to send to the IRS should they ask.
Letters like this are nothing to be afraid of, especially since you have all the detail information.
Even if the letter comes to you as a billing for self-employment income, you always have to keep in mind that such notices are form letters that come out of an automated computer system, meaning no one has actually looked at your return to see where else the income might be reported, so all you have to do is tell them where to look. Receiving such a notice does not mean you'll be put on some kind of list to be examined in future years, it's just the result of automated matching systems.
