I think you are right - I changed each GDAX deposit to "[In] Income" and the warnings are now GONE. Now I just need to figure out how to reconcile this mess with the 1099K I received from GDAX. I know I have to to fill out Form 8949 (Sales and Other Dispositions of Capital Assets) with the information provided by cointracking.info, and that will go on my Schedule D. But where do I reconcile the 1099K? Will that go on a Schedule C?
Assuming it's income, yes.
Those 30 payments were people paying me for a service that I offer - so would those payment be considered income? The rest the $3 million (listed on the 1099k) is just my personal trading. No one knew GDAX was going to be sending out 1099K's until the very end of 2017 (and by then, I had racked up thousands of trades).