Good questions.
“1) The 6 ajjhatta äyatana are not the 6 physical eyes, ears, nose, tongue, body, and mano indriya right? Ajjhatta äyatana are the 6 mental pasada rupa that is in the gandabba? Specifically cakku pasada rupa, sota pasada rupa, ghana pasada rupa, jivha pasada rupa, kaya pasada rupa, hadaya vatthu?”
Correct.
“2) Are all those 6 ajjhatta äyatana made up of mano rupa? Even the hadaya vatthu?”
No. Those are actually (barely) above the “mano rupa” or “vinnana” stage. They are at suddhashtaka stage (the smallest “rupa rupa” or “vanna rupa”).
– They are created by kammic energy at the cuti-patisandhi stage, when a new bhava is grasped.
– Those are really the “essence” of a living being.
– In the case of a brahma, that is basically all there is. Of course, there is arising of thoughts (cittaja kaya), and the utuja kaya (“aura body”) that is due to the cittaja kaya.
– That is also the essence of a human or animal gandhabba. However, a gandhabba can “absorb” aroma and acquire a trace of matter, the finest state of a karaja kaya. Our karaja kaya (physical body) is the VERY DENSE form of that karaja kaya.
“3) The 6 bahiddha äyatana are also not the 6 physical sense faculties either right? Bahiddha äyatana are the rupa rupa from the material world that enter the 5 physical sense doors(eye, ear,nose, tongue, body) and the mano rupa from the mental world that enter the mano indriya?”
Correct. Very good observation.
“4) The 6 external physical sense doors(eyes, ear,nose, tongue, body, mano indriya) are not what does the actual sensing right? They are merely the doors, the gateway for either rupa rupa/mano rupa to enter these doors and eventually transfer to the 6 internal mental sense faculties? Because it’s these 6 internal mental sense faculties(pasada rupa and hadaya vatthu) which does the actual feeling/sensing of the material and mental world?”
Yes. Our physical eyes, ears, nose, tongue, body, and the mana indriya just help in getting the “signals” coming from bahiddha äyatana to the ajjhatta äyatana.
“5) Why are they called ayatana instead of indriya? Because isn’t everything we sense initially neutral thus are indriya rather than ayatana?”
Those indriya become ayatana due to avijja and tanha: We not only “see”, “hear”, etc, but also attach our likings/cravings to those signals.
– That is why only an Arahant uses them as indriya.
“Indriya and Āyatana – Big Difference”
You are almost there in grasping the essence!