Good comments/questions, Upekkha.
You wrote: “1) Am I correct in the analysis of how punnabisankhara and apunnabhisankhara lead to dukkha? Apunnabhisankhara leads to bad kamma which leads to bad kamma vipaka which causes dukkha/suffering. Punnabhisankhara leads to good kamma which leads to good kamma vipaka, but this good kamma vipaka will not last forever and has to end which will cause dukkha/suffering.”
– That is right.
You wrote: “2) I think I may have understood how apunnabhisankhara and punnabhisankhara leads to suffering. But I can’t understand how neutral sankhara leads to dukkha. Neutral sankhara like drinking water or walking leads to neutral kamma with no future consequences, nothing good nor bad.”
– You are again correct that it is not easy to see how dukkha can arise from “neutral actions” that you mentioned. The key is to realize that one needs to first remove sufferings that are clearly seen at one’s stage on the Path.
– We need to look at this way. Anyone can clearly see the suffering that most animals go through. If one has faith in the Buddha, one will also believe that even worse suffering exists in other three apayas. Such rebirths occur due to apunnabhisankhara. They must be first stopped.
– As we can also see, there is suffering even in the human realm. A birth in the human realm is due to punnabhisankhara. As you mentioned, births in any realm end with death and suffering. So, suffering exists in ALL realms even if higher realms have relatively more “pleasures.” Thus the next step is to see the anicca nature and to see the fruitlessness of even punnabhisankhara.
– Anyone below the Anagami stage should really not worry about those “neutral sankhara.” There is the suffering associated with eating, drinking, and even breathing! All those take an effort, even though we do not think about it.
– One has to make a living to eat and drink. So, that is somewhat easier to see. But even breathing takes an effort. This can be seen when one gets to the fourth jhana samapatti and the breathing stops. That relief is seen at that time. This is why it is said that an Arahant looks forward to Parinibbana (death of the physical body.)
You wrote: “3) Same as above, I can’t understand how doing kusala kamma or doing Anapana could lead to suffering.”
– The key to realizing here is that punnabhisankhara are not the same as kusala kamma. Punnabhisankhara are punna kamma and lead to rebirths in “good realms.” Rebirth process is stopped with kusala kamma. So, real kusala kamma and correct Anapanasati (with the comprehension of anicca nature) lead to the stopping of the rebirth process (via four stages of magga phala).
– Of course, one MUST do kusala kamma and/or punna kamma (both come under “good deeds”). The first goal is to stay away from the apayas. In fact, before the Sotapanna (at least the Sotapanna Anugami) stage, most kusala kamma one does are only punna kamma.
– That is a bit of a deep point. When one does a punna kamma one may have at least a subtle expectation of a “good return” for that action. Punna kamma are the “good actions” done before grasping Tilakkhana. The same actions automatically become kusala kamma when one can “see” the unfruitfulness of rebirths in any realm (i.e., anicca nature).
– Some punna kamma AUTOMATICALLY becomes a kusala kamma when one gets to the Sotapanna Anugami stage. Then as one makes progress, more and more types of punna kamma will become kusala kamma.