Question Answer

What is the status of kissing the thumbs upon hearing the mubarak name of Rasulullah sallallahu alayhi wasallam during the adhan? Is the hadith that is normally furnished as proof for this practice a fabrication (mawdu`)? What is the meaning of mawdu` hadith?

Replying to the adhan is a Sunnah Muakkadah which is close to Wajib. Kissing the thumbs upon hearing the blessed name of Rasulullah sallallahu alayhi wasallam is not proven from any sahih (authentic) Marfu` Hadith.
There is a hadith mentioned in Kitab ul Firduas. Shah Abdul Aziz Muhaddith Dehlawi has written about this kitaab that it contains many fabricated (Mawdu`) ahadith. A mawdu hadith is that which was not uttered by Nabi sallallahu alayhi wasallam but was falsely attributed to him (by some other person). This narration is also found in Kanz al Ibad and Fatawa Suffiyah.
However, Alama Shami has written in Radd ul Muhtar that Fatawa Suffiyah is not an authentic book; and that fatwa cannot be given from it. Alama ibn Abidin has written the following in the discussion of the narration:
Allamah Jirahi has discussed this question in detail and concluded that there is no marfu` hadith from which it can be established that kissing the thumbs is a sunnah or mustahab practice (Shami, v1 p267)

What is the proof for the two adhans of Jumu`ah ?

Initially, there used to be only one adhan for Jumu`ah. When the number of people attending Jum`uah began increasing, then by the order of some of the Khulafa Rashidin, two adhans were given (Sharh al Bukhari)
Saib ibn Yazid says: "The adhan on Friday, initially, used to be when the Imam sat on the mimbar. This continued during the era of Rasulullah sallallahu `alayhi wasallam and that of Hadrat Abu Bakr and Hadrat Umar. When the number of people increased during the time of Hadrat Uthman, he added the third adhan* at a place called Zawra (Fath ul Bari, v2 p326)

In the incident where the Bedouin urinated in the Masjidun Nabawi in the presence of our Rasool (Sallallahu Alaihi Wasallam), did our Prophet (Sallallahu Alaihi Wasallam) personally clean it up or did the Sahabah do so?

In the narrations of Bukhari and Muslim, it is not mentioned clearly who had cleaned up the mess the Bedouin had made. It is mentioned in Sahih al-Bukhari that a Bedouin urinated in the Musjid and the Sahabah stood up to confront him. Nabi (Sallallahu Alaihi Wasallam) asked them to leave him and not to stop him. Thereafter he asked them to bring a bucket of water and pour it over the soiled place and said, "You all (including himself) are meant to be easygoing with people and not difficult". (Sahih al-Bukhari, Hadith #: 6128)
عن عبيد الله بن عبد الله بن عتبة أن أبا هريرة أخبره أن أعرابيا بال فى المسجد ، فثار إليه الناس ليقعوا به فقال لهم رسول الله - صلى الله عليه وسلم - "دعوه ، وأهريقوا على بوله ذنوبا من ماء - أو سجلا من ماء - فإنما بعثتم ميسرين ، ولم تبعثوا معسرين". (صحيح البخاري، الحديث: 6128)
However, in Musannaf ibn Abi Shaibah, it is mentioned clearly that Nabi (Sallallahu Alaihi Wasallam) was the one who poured the water over the soiled place. (Chapter of the one who washed away the urine in the Musjid).
من كان يغسل البول من المسجد عن أنس أن أعرابيا بال في المسجد فدعى رسول الله صلى الله عليه وسلم بذنوب من ماء فصبه على بوله. (المصنف لابن أبي شيبة).

Recently, it has been discovered that urine of animals and humans contain medicinal properties which may be used to cure certain sicknesses. Kindly clarify the Islamic ruling on using urine for such purposes

Allah Ta'ala has created man as the best of creation and has blessed him with noble character with a balanced and pure temperament where he has a natural dislike for that which is impure.According to the Fuqahaa (Muslim Jurists), urine is impure and filth and is not permissible to consume. It is narrated on the authority of Abu Wa'il that the learned Sahabi, Abdullah ibn Mas'ood (Radiallahu Anhu) said, "Certainly Allah has not placed your cure in those things which he has ordained Haraam". (Sahih al-Bukhari, Hadith #: 15).
However, the prohibition of consuming medication containing Haraam ingredients will be relaxed if a proficient Muslim doctor advises that:
The patient's life is in danger if medication with Haraam ingredients is not administered;
There is no other permissible, Halaal alternative.
It is known with certainty that the cure for this sickness is in medication that contains Haraam ingredients.
The Sunnah of reciting the three Quls and its benefits

Following the practice of Rasulullah (sallallaahu alaihi wasallam) with regards to reading the 3 Quls thrice and rubbing over one's body, what is the Sunnah method for this practice? And when should this be performed?

It is narrated on the authority of Aa'ishah (Radiyallahu Anha) that Rasulullah (Sallallahu Alaihi Wasallam) used to recite Surah Ikhlaas, Surah Falaq and Surah Naas before retiring to bed. He used to blow into his hands after recitation and rub his hands over his body. (Tafseer ibn Kathir).
عن عائشة أن النبي صلى الله عليه وسلم كان إذا أوى إلى فراشه كُل ليلة جمع كفيه، ثم نفث فيهما فقرأ فيهما: " قُلْ هُوَ اللَّهُ أَحَدٌ " و " قُلْ أَعُوذُ بِرَبِّ الْفَلَقِ " و " قُلْ أَعُوذُ بِرَبِّ النَّاسِ " ثم يمسح بهما ما استطاع من جسده، يبدأ بهما على رأسه ووجهه، وما أقبل من جسده، يفعل ذلك ثلاث مرات. (تفسير ابن كثير).
It is recorded in Abu Dawood that Rasulullah (Sallallahu Alaihi Wasallam)said, "Whoever recites the Qul Huwallahu Ahad, Qul A'uzu Birabbil Falaq and Qul A'uzu Birabbinnaas three times each every morning and evening, this will be sufficient for him for everything. (Abu Dawood, Hadith #: 5084)
عن معاذ بن عبد الله بن خبيب عن أبيه أنه قال خرجنا فى ليلة مطر وظلمة شديدة نطلب رسول الله صلى الله عليه وسلم- ليصلى لنا فأدركناه فقال أصليتم فلم أقل شيئا فقال « قل ». فلم أقل شيئا ثم قال قل فلم أقل شيئا ثم قال قل فقلت يا رسول الله ما أقول قال (قل هو الله أحد) والمعوذتين حين تمسى وحين تصبح ثلاث مرات تكفيك من كل شىء (سنن أبي داود، الحديث: 5084)
In this Hadith, it is mentioned that by doing this, "this will be sufficient for him for everything". This means that if a person practices on this Hadith with full faith and with punctuality, he will be saved from all evil including black magic and evil spirits.