It is my hope that you are truly searching for answers. It is my hope and prayer that some of what I offer will help you in your search.
Jesus' followers--distraught, sad, and disillusioned--had visions in what we now call altered states of consciousness, a condition that can be induced by fasting, sleep deprivation, and fatigue.
Regarding psychological phenomena we must first define terms. If we are talking about illusions then we are dealing with distorted perceptions of reality. If we are talking about hallucinations, then we are dealing with false perceptions of something that really does not exist. If we are talking about delusions, then we have false beliefs that can be demonstrated as false once contrary information is presented.
First, hallucinations are not group occurences, but are unique to individuals, like dreams. Hallucinations do not explain the empty tomb. Hallucinations do not explain the conversion of Paul who did not have the mindset of a follower of Christ at the time of Jesus' death and resurrection. Hallucinations do not explain the conversion of James, the brother of Jesus, who has a skeptic, and was not a follower of Jesus during Jesus' ministry. There are too many variances in the appearances of Jesus. The appearances included men and women; they were seen by groups and individuals; they were affrimed by friend and foe; there were appearances to hard headed Peter and soft hearted Mary Magdalene; the appearances were indoors and outdoors; there was not just one appearance, but many appearances over the period of 40 days.
Second, delusions do not explain the empty tomb. Delusions do not explain the conversion of Paul. Candidates for delusions believe something so deeply that their logic gets screwed up. Paul was so commited to his Jewish faith that he was hostile to Christians. Why would Paul want to follow a rightly executed blasphemous false prophet, and lose his eternal soul, if the resurrection was a delusional event? Delusions do not explain the conversion of James the brother of Jesus for the same reasons.
If what you mean by vision, you mean an "objective" vision, then Jesus is truly risen. Jesus was actually sin but not in a physical state. Jesus then survived death and the consequences are the same as the bodily resurrection; God exists and Christianity is true. Further, this objection does not dispute the resurrection, but disputes the form of it, material or immaterial. If the visions are subjective, then they were hallucinations or delusions. I have addressed those objections above.
I think that Paul probably had a vision of Jesus also, though I am not sure of the mechanism that caused this (epilepsy, feeling of shame about persecuting Christians, etc.)
If you have any evidence of Paul suffering from epilesy please present it. While I have just completed a rather extensive study of the resurrection of Jesus, it is possible that I missed something. That said, I find no scholar that remotely hints at Paul having epilepsy.
If Paul felt any guilt over his persecution of Christians, we find no evidence of it. In fact, Paul's own writings indicate that he was rather proud of his actions against the Christians and was very content in his Judaism (Phil. 3:5-6). Even if Paul felt guilt to the point of conversion, that does not explain the Jesus' appearances to the other disciples and the conversion of James the brother of Jesus. Paul's guilt does not account for the empty tomb.
My thought is that the gospel ends this way on purpose as a way to explain why it took so long to proclaim the empty-tomb message.
This is a rather silly statement, because the "empty tomb" message was a message that the Jewish religious leaders had to account for it by bribing the tomb guards. Further, 50 days is such an incredibly loooooooong time to concoct an "empty-tomb message." Peter referenced the resurrection in his Pentecost sermon (Acts 2:29-36).
whether Paul's belief that Jesus' rising as a "spiritual body" (1 Cor. 15:44) meant that Jesus' physical body was left behind (thus, no empty tomb, if Jesus was even buried in a tomb) or whether he believed that Jesus' physical body was changed into a "spiritual body," whatever that meant to Paul.
Paul, and the rest of the NT writers believed in a bodily resurrection. If they had not believed that, and wished to communicate that, they had vocabulary available that would have communicated this belief.
Further, the empty tomb is a fact that has been affirmed by approximately 75% of the scholars studied by Gary Habermas (The Case for the Resurrection of Jesus).
Regarding your issues with the gospels, I do not believe that they are problems. The reason is that each writer was interested not in total harmony with the other writers (which would actually be a strike against their verasity), but with communicating with his intended audience. This fact should not be held against the authors.
what happened to make the disciples believers, whether there was an empty tomb, what explains the empty tomb,
I believe that a real resurrected Jesus accounts for all of these things. It is the only event that could transform those fearful early disciples of Jesus in to men and women that turned the world upside down (Acts 17:6). There was an empty tomb. Unless you have an alternative explanation, like the Jesus Seminar. What explains the empty tomb? In my opinion only the resurrection of Jesus explains the empty tomb. All other opposing theories or combination of theories fall far from offering any sort of effective explaination for the empty tomb.
how did Mark's gospel end
Based on everything scholarly I have read (liberal and conservative), Mark's gospel ends with verse 8. I don't have aproblem with it, because this is pointed out in every Bible translation, including that abomination, the New World Translation, I have read. I do not believe that the additional verses affect any core doctrine, because we have accounts that are more full in the other Gospels.
I have looked extensively at the resurrection for the past few months. My trust in the accounts has grown stronger. Stronger than before starting on this task. I hope that everyone does this, it is a task that is deeply rewarding.