I'll try to answer as many of your points as possible and provide context.

My background on the Armenian Genocide is reliable in my opinion, I've read several primary sources from the period (both from the Ottoman and the Armenian/Russian perspective) and I've read Turkish documents and eyewitness accounts. I'll start by saying I'm not in the business of relying all my evidence on dramatized doctored photographs depicting Mustafa Kemala sitting over a starving child (it was actually a dog in the original photo) or a supposed Turkish man taunting starving children with bread.

I rely less on overhyped documents meant at 'proving intent', like an explicit message from Talaat or Enver. There are hundreds of other ways to prove intent and one is by using logic and looking at the facts on the ground. So I cannot speak on these documents since I'm not an expert on their authenticity, so I'll leave that to someone else, and begin at your third point.

So the Germans were allies of the Ottomans, and they deliberately ignored the persecution of Armenians because they were so bent on winning the war at all cost that they allowed that to occur in order to keep relations good and the Ottomans in the war. The Ottoman narrative after all was that they were "fighting pro-Russian separatist rebels (i.e. Armenians)" and that narrative suited the German high command. Is there some truth in this narrative? I'll address that after... What I wanted to add is individual German soldiers like Armin T. Wegner, who were engineers stationed in Syria witnessed the mass deportation of Armenians southward and the death of many of them. These soldiers were appalled at what they witnessed, not because they were sympathetic "Christian Europeans" (stay with me...) but because they were humans with empathy. In Cuatro años bajo la Media Luna (1925) by De Nogales Mendez (a Christian Venezuelan Ottoman officer) he mentioned that many German doctors and engineers tried to take secret photographs of the Armenians, but the Ottomans tried to maintain as much secrecy as possible about the whole operation.

The next point is about the Armenians rebelling. So did they rebel before or after? Well, the rebellion began in April 1915 around Van however the Ottomans in many ways provoked a reaction from the Armenians through very harsh measures and policies taken before. I'll give you a few examples... At the beginning of the war the Armenians were not automatically suspected of disloyalty and treachery, and in fact Enver wanted to 'liberate' the Muslim-Caucasus and use the Armenians as possible allies. However the Armenians were put into a position where they were forced to pick a side, and ultimately many sided with Russia and in the Battle of Sarikamish (Dec 1914 - Jan 1915), the Ottomans lost most of their army in the mountains and Enver's plans to invade the Caucasus early-on was crushed. Armenian volunteer battalions fought on the Russian side (however most of these 'Armenians' were Russian citizens, not Ottoman ones..) and in response Enver released Directive 8682 in February that banned Armenians from serving in the army or police and required them to join the so-called labor battalions that were practically worked to death carrying supplies for the army and along the way many died. Mendez mentioned in Cuatro años.. seeing these labor workers, and bodies of fallen ones lying on the side of the road totally discarded and the ration of bread was very low. (I can try to find the page number if you request it, I don't have the copy of the book on me at the moment)

Mendez also mentioned passing through Erzurum on his way to the Caucasus front sometime in February or March, and while he went through these towns the local Armenians (who had boarded up their homes and business out of fear) noticed he was a Christian and would run towards him and beg him to stay and protect them. The Armenians had experienced persecution before by the Ottoman authorities, and many survivors remembered the 1890s massacres under Abdul-Hamid, and the point is many Armenians were worried about a similar event transpiring.

Now we get into April 1915, and this is when the Armenian rebellion of Van occurred, the first organized rebellion. Coincidentally Mendez provides one of the best accounts of the battle and he commanded an Ottoman expeditionary army from the start. He recounts that it's unclear who started the battle, but he attributed it to many provocations taken by the CUP governor named Djevdet Bey. For example Armenian homes were being raided by his police to search for hidden weapons in accordance with Directive 8682 and during these raids many people were killed, and a few Ottoman soldiers were ambushed and killed in one incident which helped to spiral things out of control. In the end all the Armenian quarters in towns around Lake Van were being attacked, Armenians were being killed on the street, and the Armenian rebels had taken control of the city of Van. Mendez took a ferry from the north of Lake Van to the south and along the way he saw his Ottoman escorts murder two Armenian laborers with gunshots and dump their bodies overboard and he reached the island of Aghtamar where he saw the bodies of dead Armenian priests and Kurdish rebels demanding from the Ottoman soldiers more ammunition. (the Ottoman army relied on these Kurdish and Circassian irregulars to fight the Armenian rebels) Armenian historiography portrays the Battle of Van as an act of self-defense rather than a pre-planned event.

So to summarize, the Armenians rebelled but after many provocations and the Ottomans certainly did nothing to help ease tensions as evidenced by Directive 8682 back in February before any rebellion had taken place. In any case, imagine if they did rebel at Van totally unprovoked, would that justify murdering unarmed innocent Armenian civilians just because they are Armenian? That is what happened and it was a genocidal act meant at ethnic cleansing the Armenians from the Van region.

Regarding graves, many have been discovered especially in northern Syria. I know of a few grave sites in today's eastern Turkey, and many of the bodies were dumped into caves, crevasses etc. Mendez recorded that around the towns of Bitlis and Mush, he was told by an Ottoman official that the Armenians there were brought to the hills south of the city and killed and buried in mass graves. In another incident elsewhere Mendez recorded he saw an Ottoman official point to a cave where they had thrown Armenian bodies in. Truthfully I think there weren't as many mass executions and mass grave sites as suspected and most Armenians were scattered around when they died because they were first deported from their towns and then marched southward to Syria where many died indirectly along the way (from disease and malnutrition) and were left on the side of the road to be buried by the locals.

Regarding the Greek and Assyrian genocides, those were occured at about the same time as the Armenian one. Most Greeks were lucky because they did not live near the conflict zone in the Caucasus (whereas the Armenians and Assyrians did) and since Greece was neutral and King Constantine was aligned with the Germans, the Ottomans did not pursue an anti-Greek policy early on. However Pontic-Greeks were more often than not grouped together with Armenians. After 1915 Assyrians and Nestorians etc. were all branded as possible Christian rebels (a fifth column) so they were persecuted as well but not to the extent as the Armenians since they already lived in the south in Syria and Iraq whereas Armenians lived more to the north near the frontline. Mendez wrote he encountered once a group of Armenians hiding who lied that they were Nestorians and were killed, so perhaps some Christian groups were more favored by the Ottomans at that one time but through the years the massacres really became anti-Christian in nature. Less Greeks and Assyrians perished and that is why their plight is often overlooked.

As for the Treaty of Sevres (1920), it was harsh but this was just as all WW1 peace treaties were. Ask a Hungarian about Trianon, that treaty stripped Hungary of most of its land and made them a small country with millions of Hungarians living outside its borders. Did Hungarians rebel and start killing people? No. The Turks went about it a different way and decided to rebel against the unfavorable treaty after the war had ended. The point is Sevres was not a conspiracy to "destroy" Turkey by "Christian-Europeans" who hated them, that is a myth. Greece wasn't even given Constantinople in the treaty and instead it was made into an 'international-zone'. The Ottomans had to recognize the Armenian genocide in the treaty and prosecute war criminals, however after Mustafa Kemal in 1921 came to power he ended the trials, got back the 64 Ottoman officials (the so-called Malta exiles) held in Malta by threatening to execute 21 British soldiers (among them the brother of a British general), and this happened before any tribunals took place. Kemal then pardoned the war criminals and destroyed most of the evidence because he wanted to move on..