Form 5329

That is all, TurboTax will calculate your penalty and include the form with your return.  

Does the income then appear on 1040 Sch 2? It seems I would need a 1099R substitute to report the income and calculate tax as if the RMD had been made. 

No, you report the distribution in the next year, when you receive it. You receive a penalty for missing it in the current year, but request abatement of the penalty on Form 5329.