The hadith in withstanding bad leaders and governors are almost countless, including from Sahih:
Some came to the prophet and asked "Oh prophet of God, what if we get Amirs who are unjust and corrupt and wouldn't give us our rights?" The prophet responded: "Listen and obey, for you will be rewarded for what you do, and they will answer (in judgement day) for what they do".
And then there is "Whomever hates something from his Amir, he should stay on it in patience, for whomever goes against the Amir and dies, he has died the death of Jahiliya (outside the fold of Islam)" Sahih Al-Bukhary and Muslim
Then there is MOST FITTINGLY: The prophet said "There will be leaders after me who do not heed my guidance and do not abide by my sunnah, but there will be men who rise against them, they will have the hearts of devils inside the bodies of humans." Anas -ra- said: "What should I do then if I live to see this?" the prophet replied: "Listen and obey the leader, if he lashes your back and takes your money, you listen and obey."
As for the scholars you mentioned, Yes people I know too were jailed and lashed and shot and discredited. I studied in Abu Dhabi and Saudi Arabia and Egypt and now I am in Malaysia's Islamic University, over 11 years studying actively, and I am Egyptian originally so I know the hardship of bad government. But the government that comes with blood over the old one is no good, because even if it happens and was miraculously good and fair, it puts me in hell instead of heaven if I fight with it because I would have so many broken sahih Hadith from the prophet that state clearly I will be out of the fold of Jamaa and out of the fold of Islam! My brother those scholars did not take up arms and break ranks and shed the blood of muslims despite all that hardship they are facing, so believe me I know what I am talking about and they too.
As for Ibn Taymeyya, well here you go:
( ولهذا كان المشهور من مذهب أهل السنة أنهم لا يرون الخروج عن الأئمة وقتالهم بالسيف، وإن كان فيهم ظلم، كما دلت على ذلك الأحاديث الصحيحة المستفيضة عن النبي (r) لأن الفساد في القتال والفتنة أعظم من الفساد الحاصل بظلمهم بدون قتال ولا فتنة، فلا يدفع أعظم الفسادين بالتزام أدناهما ولعله لا يكاد يعرف طائفة خرجت على ذي سلطان إلا وكان خروجها من الفساد ما هو أعظم من الفساد الذي أزالته... ولذا لا يصح قتالهم بالسيف حتى لدفع ظلم). (منهاج السنة، (3/391) ط، مكتبة المعارف).
"It is known from the math-hab of the people of Sunnah that they do not approve of mutiny on leaders and fighting them with the sword, even if they are unjust, as proven by a multitude of correct authentic hadiths from the prophet -pbuh-, because the corruption and fitna in the fighting is far greater than the corruption that is there without fighting, so the lower corruption needs to be headed, and no group has ever mutinied on their leaders without producing a corruption that is far greater than the one it removed.... It is therefore forbidden to fight the leader by the sword even if they are unjust" The manhaj of Sunnah 3/391
That is Ibn Taymeyya. Otherwise, his Jihad against the mongols was because they were an invading force that never really converted to Islam and refused to even marry from muslims, and did not uphold prayer or anything!
What about Ahmed Ibn Hanbal, the source of jurisprudence for both Ibn Taymeyya as well as Ibn Abdul Wahhab:
السمع والطاعة للأئمة وأمير المؤمنين البر والفاجر من ولي الخلافة، واجتمع الناس عليه ورضوا به، ومن غلبهم بالسيف حتى صار خليفة وسمي أمير المؤمنين
"Listening and obeying to the leaders and to the Amir whether they are decent or fajer (abhorent) whomever has the leadership or the people are around and accepted, or whomever won over them by the sword until he became leader and was called Amir Al-Mo'menien"
Don't make me start with Al-Albani's sections on this matter, they are too many and I am getting sleepy.
All the rest of the stuff you are talking about of "working with those who are kuffar" or "not applying sharia" and all that are all not excuses for calling people as apostates, making their blood halal, and turning to war and mutiny against muslim governorsunder the guise that they are criminal or unjust, let alone that they are actually calling to peace and decided to rule by Shareah.
If you are not convinced, that is your own undoing. This is the established principals of Islam from the prophet -pbuh-, from his sahaba and from the most established respected scholars of that and this time, including the entirity of my colleagues.
Any "great" Ulema who want to go against this, and against direct sahih Hadith statements, can keep their greatness to themselves.
Allahumma ballaght, allahumma fash-had.

then after all that discussion it comes down to three issues where we should hone in on our discussion,
1. is that you hold it is not valid to rebel against a ruler?
2. allying with the kuffar is not kufr when he is fighting your brother
3. and not ruling by the shariah are not kufr
would you agree from reading back on our comments that these are our main disagreements and if one of us could convince the other on all three from the Quran and sunnah and what comes from that then we would have solved our differences?
as for point 1, it is really an extension of 2. and 3. this is because i agree it is not allowed to rebel against a ruler who is a fasiq, even if he is oppressing you.
but if a ruler becomes a kaffir then it is allowed as you mentioned yourself. agreed?
so let us concentrate on the issues of whether allying with the kuffar and not ruling by the shariah of Allah are matters which take the ruler out of islam.
if we can agree to this then we can inshallah continue and you can bring your evidences and me mine and each try to show the other we are correct, as you are training to be an alim this should really be no difficulty for you.
