بسم الله الرحمن الرحيم
(1) There are two rakahs fardh in Jumuah which each Muslim knows. It is proved from Hadiths, common practice and unanimity of ummah. Before the two fardh rakahs of Jumuah four rakahs are sunnah muwakkidah and after the fardh of Jumuah four rakahs are sunnah muwakkidah and two rakahs nafl. Imam Abu Yusuf (may Allah have mercy on him), who is disciple of Imam Abu Hanifah (may Allah have mercy on him) and a great Imam of Hanafi Fiqh, says that there are six rakahs sunnah muwakkidah after the fardh of Jumuah.
(2) When Imam comes for khutbah then it is forbidden to offer any salah or talk. Hence one should not start any salah. Yes, one should make up the missed four rakah sunnah after offering fardh.
(3) It should be offered after the fardh of Jumuah.
(4) One should not raise his hands in Khutbah for dua or say Amen. It is forbidden. A hadith state:
اذا خرج الامام فلا صلاة ولا كلام .
Yes, one is allowed to reply the azan of khutbah. It is known by the hadith related by Hadhrat Emir Muavia (may Allah be pleased with him) in which he replied the azan of muezzin while sitting on the member and said:
يا ايها الناس انى سمعت رسول الله صلى الله عليه وسلم على هذا المجلس حين اذن الموذن يقول ما سمعتم منى مقالتى (بخارى ج 1 ص 125)
But it is better to reply it in heart.
Allah knows Best!
Darul Uloom Deoband