What is the ruling of Islamic Law on supplicating with other than the transmitted (Ma'thur) supplications in prayer?
All praise is due to Allah, and peace and blessings be upon our master, the Messenger of Allah.
It is permissible to supplicate (make du'a) during the prayer for anything from the affairs of religion or worldly life, and the prayer is not invalidated by doing so.
Shaykh al-Islam, the Imam an-Nawawi, may Allah have mercy on him, says: "Our madhhab [i.e., the Shafi'i madhhab] holds that it is permissible for a person to supplicate during it [the prayer] with anything that is permissible to supplicate with outside the prayer, from the affairs of religion or worldly life. He may say: 'O Allah, grant me wholesome sustenance, offspring, a house, and a beautiful young wife' — describing her; or: 'O Allah, free so-and-so from prison,' or 'destroy so-and-so,' and other such things — and none of this invalidates his prayer according to us. And this is also the view of Malik, ath-Thawri, Abu Thawr, and Ishaq." [Al-Majmu', Vol.3/P.454]. And Allah, the Exalted, 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.
Can someone who begins a voluntary fast break it?
It is preferable for someone who begins an act of worship not to break it.
Allah the Exalted has said {what means}: "and let not your [good] deeds come to nought!" [Muhammad/33].
However, if a person starts a voluntary fast (nafl) and needs to break it, they are going against what is preferable, but there is no sin upon them.
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.