I’m not a master at calculating APRs, but I can give you a resource that I use that is really helpful. You can search for the program called APRWIN which is offered by the OCC and is Free. It’s really easy to use, just follow the prompts and it will let you know what the APR should be. It’s a great tool to double check your loan origination software.
From your questions I think you might have the requirements for HPML confussed a bit. I know it was a big issue when it first came out about having to use the highest payment within the first 7 years on HPML loans, but that was in determining your borrowers ability to repay. I don’t think it has anything to do directly with the APR. You should only have one APR amount.
I highly suggest checking out the APRWIN program; I think it will really help you with what you need.