I know nothing...nothing...
...about Yuri Gagarin's death, so I am not going to comment on what might have happened that day. So I will only confine my argument to your points of conspiracy.
Aircraft - I gather from your comment that you are Russian or otherwise former-Soviet, and I don't mean to be offensive or get into nationalistic arguments, but this was a MiG-15 (I assume UTI). Soviet equipment of that period don't exactly have the best of safety or reliability records. It could have easily been a mechanical or maintenance fault that cause a crisis in the cockpit. Or it could have been a similar fault that prevented ejection of tanks or seats. Such ejection failures are still reasonably common today, usually of tanks and weapons rather than seats. In addition, aircraft cockpits of all nations in this period often weren't very ergonomically designed for usability. How well trained/competent were the maintenance engineers working on the aircraft? Conscription-based militaries don't have the best of records when it comes to training or competence around complex machinery.
Pilots - Experts are no less likely to make errors than novices, just for different reasons. It is their very familiarity with a task or device that can cause errors. Overconfidence is a killer. Expertise is also no guarantee that a problem encountered can also be overcome. These were two human beings, not perfect and infallible fighter gods. Maybe the problems were too serious for either of them to remember about ejecting the drop-tanks? Maybe they didn't eject because they thought they could recover the aircraft?
Flight Schedule - I can think of a non-state-sponsored-conspiracy laden reason why there is no documentation: It got lost. Office documentation, even important ones, go walkabout all the time. It just needs someone to carelessly misplace it. Someone may have made it lost, but what would be the point? You said that Vladimir Seryogin was the senior officer on the base. If I was creating a conspiracy to crash the plane (one that required A LOT of on-site conspirators) I would get someone to testify that Gagarin and Seryogin went on an unscheduled joy flight. Furthermore, if this was a state conspiracy how easy would it be to enter the flight into the schedule normally, or even just CREATE a schedule? I cannot see that this is an issue.
Flight Preparation - See my point above about overconfidence. In addition I will point out that walking around an aircraft isn't going to catch everything, and also that assumptions about a device's readiness or condition isn't confined to novices.
Impact Angle - Surely an impact crater can't show you what was happening to the aircraft in the lead up to impact? I'm not an expert, but I would think that all it can show is what the aircraft attitude was, direction of movement and a rough estimation of velocity AT THE MOMENT OF IMPACT. It cannot say whether the aircraft was under control, partial control or no control. As I said above, perhaps Gagarin thought he had gotten the plane back under control and just ran out of altitude. Given that the MiG-15UTI didn't have a flight data recorder or a cockpit voice recorder, you really can't say what was happening or what the impact site might mean.
Conclusion - The USAF publishes reports of their air crashes which the public can read for themselves. I suggest you go and look at them because it may help you. These reports show: modern/new aircraft have mechanical failures, otherwise well designed aircraft have fatal flaws, very well trained engineers make maintenance mistakes, experienced pilots make silly novice mistakes, experienced pilots show off and kill themselves and others, experienced pilots often don't eject when they have the chance because they think they can get the aircraft back under control, and that inattention to routine tasks/procedures tend to be magnified by the unexpected.
The only thing exceptional about the Gagarin/Seryogin crash was the occupants. I imagine that none of my arguments will have an effect on your opinion that this was a state-sponsored murder, so I will ask one last question: Why? There is no reason for Gagarin to be murdered. He wasn't a "trouble-maker" or an activist. It may be propaganda, but what I've seen is he was a committed patriot, and a national hero that the government tried hard to keep alive because he was such an effective icon for communism. To a government tool, alive he could continue to be trotted out for patriotic duty, just like Neil Armstrong. But dead he is a statue and a face for postage stamps and bank notes.