What is the ruling of Islamic Law on sitting between the two prostrations, and what is the ruling on the dhikr recited during it?
Praise be to Allah, and peace and blessings upon our master, the Messenger of Allah.
Sitting between the two prostrations (al-jalsah bayna al-sajdatayn) is one of the pillars (arkān) of the prayer, while the dhikr recited during it is Sunnah according to the Shāfi'ī scholars. It is recommended (mustahabb) to say what was narrated from Ibn 'Abbās (may Allah be pleased with him), who said: "The Messenger of Allah (peace and blessings be upon him) used to say between the two prostrations in the night prayer: 'Rabbi ighfir lī, warhamnī, wajburnī, warzuqnī, warfa'nī' (My Lord, forgive me, have mercy on me, make good my deficiencies, provide for me, and raise me)." If one were to say a different supplication instead, such as "Rabbi ighfir lī" (My Lord, forgive me), the prayer would still be valid.
If the worshipper omits this dhikr between the two prostrations, whether intentionally or out of forgetfulness, their prayer remains valid and nothing is required of them, though they miss the reward of following the Sunnah. Leaving it out does not necessitate the prostration of forgetfulness (sujūd al-sahw).
It is stated in Hāshiyat al-Bājūrī 'alā Sharḥ Ibn Qāsim 'alā Matn Abī Shujā' (Vol.1/P.298): "The eleventh — i.e., of the eighteen pillars — his statement: 'sitting between the two prostrations,' meaning even in a supererogatory (nafl) prayer... his statement: 'with the supplication that has been narrated concerning it,' meaning: 'Rabbi ighfir lī, warhamnī, wajburnī, warfa'nī, warzuqnī, wahdinī, wa 'āfinī' (My Lord, forgive me, have mercy on me, make good my deficiencies, raise me, provide for me, guide me, and grant me well-being). Al-Ghazālī added: 'wa'fu 'annī' (and pardon me). Al-Mutawallī also added: 'Rabbi hab lī qalban taqiyyan, naqiyyan min al-shirk, bariyyan lā kāfiran wa lā shaqiyyan' (My Lord, grant me a heart that is God-fearing, pure from associating partners with You, innocent, neither disbelieving nor wretched)."And Allah, the Most High, knows best.
What is the ruling on performing the standing (qiyām) and bowing (rukū‘) portions of the prayer normally, while performing the prostration (sujūd) seated due to knee pain?
All praise is due to Allah, and peace and blessings be upon our master, the Messenger of Allah ﷺ.
If performing sujūd (prostration) in prayer causes the worshipper pain in the knees, then it is permissible for him to perform it through gesture (īmā') while seated, since Allah, Glorified and Exalted is He, has lifted hardship from His servants. On the authority of ‘Imrān ibn Ḥuṣayn (raḍiyallāhu ‘anh), he said: "I suffered from hemorrhoids, so I asked the Prophet ﷺ about [how to perform] the prayer, and he said: 'Pray standing; if you are unable, then sitting; and if you are unable, then on your side.'" [Ṣaḥīḥ al-Bukhārī]
If the valid excuse later subsides, the worshipper is then obligated to perform the prayer with all its pillars and conditions fully observed — including standing, rukū‘ (bowing), and sujūd (prostration). And Allah, the Exalted, knows best.
What is the ruling on using a miswak (tooth-stick) during the day in Ramadan?
It is permissible to use a miswak before noon while fasting. However, according to the Shafi'i school, it is disliked (makruh) after noon in order to preserve the natural effect of fasting in the mouth, as the Prophetﷺ said in authentic hadith:
"The breath of a fasting person is more pleasant to Allah than the fragrance of musk."
How should I deal with the whispers of the devil with regard to ablution and purity?
Whispers in ablution are from the devil, and so you should take refuge in Allah from the devil`s evil suggestions that aim to distort the religion. Thus, once an organ is completely pure, don`t question its purity since having whispers doesn`t mean that the purity is invalid as it has already been established.