Would it be better to leave money in the 529 or ESA for unqualified withdrawal?
The 529 will give you additional versatility, as the Coverdell ESA must be liquidated and paid to the child when they turn 30. On a 529 Plan you can name another family member as beneficiary and use those savings for other expenses down the road.
How would the withdrawal be taxed or penalized?
It's not clear whether you have withdrawn assets in the amount of the Florida Bright Futures scholarship, or not. If you haven't, then you can withdraw up to that amount without incurring the additional 10% non-qualified withdrawal penalty, though earnings will still be subject to tax. Any amount withdrawn beyond that for non-qualified expenses will be taxed plus incur the 10% penalty on earnings. You may wish to consult with a tax expert given the number of moving parts you have.
Also, I goofed in 2015 and didn’t take a withdrawal for eligible expenses. Is it too late?
"The IRS has never explicitly stated that expenses must match up in the same calendar year as 529 withdrawals, but the proposal advanced by IRS a few years ago to allow some wiggle room strongly suggests that there may not be any wiggle room now (the proposal was never finalized). The "everything must happen within the same calendar year" argument is based on longstanding tax rules applying to all cash-basis taxpayers. Since you and I are cash-basis taxpayers we presumably must abide by these general rules in the absence of relief from the IRS." -Joe Hurley
Ultimately, the onus is on you to record and prove your QHEEs. I know it's not the answer you want, but the conservative interpretation of the tax code is that you need to make the withdrawal during the period in which the expense is incurred.
Good luck,
Brian