"The 1099-R still has it coded as "1--Early distribution, no known exceptions." "

The issuer of the 1099-R has not made the determination that this is a qualified distribution; that's why you see that code. I've only seen one provider giving out certification forms to keep on file.

Your client needs to confirm this qualifies.

Form 5329 is for waiving the penalty.

Form 8915-E is for taking the total taxable income in the first year or spreading it out over three years.