The IRS requires the average based on the monthly statements. I take this to mean that any month you carry the loan needs to be included in the calculation. Since you would have the refinanced loan from April through December, I would count that as nine months, just to be a little more conservative.
If the HELOC were more like a piggyback loan to buy the house, you can answer Yes to that question, as long as no money was taken out for any other purpose but the down payment.
If steps 11-13 never came up and you are above the $750k limit, you may have to delete everything out and start all over again. Sometimes if you go through and change your answers enough, some of them get stuck in the system and never really come out when you change them again. If it appears you are not getting the appropriate interest deduction, either it is too low because it is not counting all the mortgages or it is just recommending the standard deduction, then I would delete all three 1098s and re-enter them. I recommend logging out and clearing your cache and cookies after deleting them just to make extra sure that there is nothing lingering in the TurboTax worksheets when you go to re-enter them.
