Is one allowed to do Nefilas Apayim while the Torah is out of the Aron, and if yes how should it be done?
Regarding placing the head on the arm etc. – it is done as usual.
When the Sefer Torah is being moved and requires one to stand, one should not be sitting, but may continue reciting the Nefilas Apayim prayer normally. Nonetheless, according to Kabalah, Nefilas Apayim should always be done sitting. Therefore, it is best to wait and recite it once the Sefer Torah is in a stationary position.
שו״ע אדה״ז קלא, א.