Question: From what I can tell Jason went to the American embassy in Zurich, couldn't be bothered waiting in a queue, went through a door and got shouted at to stop, then ran up some stairs and climbed down the wall and escaped. What was his original purpose for going to the embassy?
Answer: The reason he didn't have to wait in "the queue" is on the sign he passes as he enters. He enters the American Citizen door because no one is in line. His passport was a "fastpass" into the embassy to avoid the police. The reason police were looking for him was because of what happened at the park. Police were looking for him. The guy at the bank called the CIA. So... the original purpose of entering the embassy was to avoid the Switzerland police. The shouting was to detain him, probably to question him about the park.
Answer: A man in the bank had called the police.
Question: What was going on with John Michael Kane's body in the morgue? Nicky said that Wombosi saw the body and didn't buy it. Were they trying to pass off the dead man as Bourne?
Answer: In fact Wombosi had shots 3 times at Bourne, and he sees that the corpse has no impacts. That is how he understands that the Americans try to fool him.
Chosen answer: Yes, exactly. Kane is one of Bourne's identities and apparently one that he used extensively during the preparations for the mission to eliminate Wombosi. Wombosi goes to see the body, but, having seen Bourne, albeit relatively briefly, realises that the body in the morgue is not the same man.
Question: What is the connection between Wombosi and Kane, i.e. how does Wombosi know/recognise Kane's corpse and make the connection to Bourne? Are we assuming that they had prior contact before Bourne tries to kill him on the boat?
Answer: If they had no prior contact, how would Wombosi have known the name Kane and to go check the morgue?
Answer: In fact on the yacht Wombosi had fired 3 bullets at Bourne. He checks that the corpse has no impacts. That is how he understands that the corpse is not the one of the killer of the boat.
Answer: Wombosi is aware that the CIA is responsible for the attempt on his life. He is also aware that the CIA attempted to kill him because of his threats to go public with information about their activities in Africa. Conklin is unaware, however that Wombosi got a good look at Bourne's face. When Wombosi sees the body in the morgue is obviously not the man he saw on the boat, he correctly suspects the CIA is trying to fool him and will likely make another attempt on his life. Wombosi and Bourne had no prior contact before that night on the boat.
Answer: To avoid the local police. They were following him and he had an American passport, so it was the quickest way to escape.
Captain Defenestrator
He was probably being wanted for the assault on the 2 police officers while he was sleeping in the park the night before.