Yes, taxes at the regular income rate on the earnings portion of any non-qualified distribution.
Every distribution is done on a pro rata basis, and the statement for the distribution will have it broken down between contributions and earnings. You get quarterly statements for the account, right? I would be surprised if the balance reported on the statements isn't broken down between contributions and earnings.
The 529 plan administrator has all the records and information needed, assuming you properly reported the components of the Coverdell when it was rolled over to the 529.