“1) When one does punnabhisankhara, are the sense faculties ayatana here as well?”
Yes. Punnabhisankhara also lead to rebirths. Even though they are in “good realms”, the rebirth process will continue. As long as one is in the rebirth process without attaining a magga phala, one is likely to be reborn in an apaya at some point.
– Yes. In this case also indriya are used as ayatana.
Another thing to keep mind is that punna kamma become kusala kamma if there is no greed or avijja associated with that act. The that would not count towards rebirth.
– For example, if one donates something out of pure compassion, that is a kusala kamma. It could become just a punna kamma if there are “any expectations” for that giving.
– In any case, one should definitely do such acts without worrying too much about that distinction. Getting rebirths in good realms is a must until one gets to a magga phala.
Regarding indriya bhavana:
You said: ‘But when we do good deeds, to eventually make these good deeds not be rooted in alobha/adosa/amoha.”
Actually, when one’s understanding increases, one’s wisdom (panna) will grow. Then one would be AUTOMATICALLY doing most deeds with panna or with understanding of the anicca nature.
– Then one would be doing more deeds with metta, karuna,mudita, upekkha.The higher the understanding, the more power those thoughts will have.
– So, that is not something easy to force. It comes with understanding.
You said: “Without good deeds, Nibbana will be difficult to attain.”
Exactly right. One should NEVER shy away from punna kamma. As our understanding grows, those will automatically become kusala kamma. We don’t need to worry whether they are punna kamma or kusala kamma.