Oswald did it. Most of your assertions are false.
There were a few eye witnesses who saw someone in the sixth floor window of the TSBD before the shooting. All of them describe a man who matches Oswald's description. The single bullet theory has been proven to be completely possible. The key is in placing the men in their proper positions in the car, with Tex Governor John Connally riding in a jump seat which put him lower than Kennedy and more towards the interior. The documentary series NOVA duplicated the single bullet shot using modern ballistics researchers and found it completely consistent with what actually happened. There were only three shots fired, or at least, no one has ever produced any evidence of more than three shots.
As for Jack Ruby, he says he killed Oswald as revenge for killing Kennedy (Ruby was a big Kennedy fan) and also supposedly to spare Jackie from having to testify at Oswald's trial. The idea of Ruby as a planned rub out by a conspiracy theory doesn't make sense. For one thing, Ruby nearly missed his opportunity because he stopped to wire bail money to a woman he knew. People in the Western Union office at the time say that he wait patiently in line and didn't appear rushed. In fact, he would have missed his opportunity but at the last minute Oswald asked to change clothes, which delayed his departure enough that Ruby was able to get there. It seems likely, from the evidence, that Ruby killed Oswald on impulse, although he was clearly contemplating it beforehand. Furthermore, the idea that Ruby was acting at the behest of a conspiracy doesn't make sense. In terms of specifics, Ruby was a braggart and blowhard. One of his friends said "If he ever knew anything important he would have told everyone he knew in about five minutes". Not exactly the person you want to use for a secret mission. And the idea of killing Oswald, on camera no less, doesn't make sense. If Oswald was "just a patsy" then he'd have no relevant information to give investigators. But Ruby, if he was a conspiratorial hit man, would have information to give them. So they'd just be trading a non-witness in custody for an actual witness.
The police swarmed Oswald at the movie theater because he had just killed a cop. Multiple witnesses saw Oswald talk to DPD office JD Tippett and then shoot Tippett when the officer got out of his car to confront him. Oswald even started to leave, then came back and shot Tippett again. In terms of Oswald's complicity in the assassination this is evidence of a guilty mind, since innocent people don't shoot cops. Learning, from emergency calls, that one of their own had been shot, the police began searching the area. The ticket clerk at the theater told them that someone had ducked inside without paying and they figured, correctly as it turned out, that this might be their guy. When they went to arrest him, Oswald tried to shoot another cop, but the cop grabbed Oswald's gun.
As for Oswald's guilt we've got pretty conclusive evidence that he shot Kennedy. First off, we know that the shots came from the TSBD. Most witnesses identified that as the origin of the shots. More importantly, forensic ballistics show that the origin point of the shots is an area centered on the sixth floor window. We also know that shots came from there because employees watching on the sixth floor heard the shots coming from directly above them. As I said, a couple of witnesses, IIRC two, saw a man who matched Oswald's description standing in the window before the motorcade arrived. Oswald was last seen by fellow employees on the sixth floor of the depository. He was not seen anywhere other than the sixth floor until after the shots were fired. When police got to the sixth floor snipers window they found that someone had stacked boxes around the window so as to screen it from the view of anyone on the sixth floor. These boxes had Oswald's fingerprints on them. They also found a manlicher carcano rifle (to my knowledge the police never claimed it was a different type of gun, although perhaps this was misreported in the press). The rifle, which was later ballistically shown to have killed Kennedy, had Oswald's fingerprints on it. The rifle was shown to have been ordered through the mail to a PO Box in the name of an A Hiddel. When Oswald was arrested at the movie theater he had an ID on him with his picture but the name Alec Hiddel. Oswald's wife, Marina, saw him with the rifle on numerous occasions and said that he regularly practiced dry firing it. Marina even took a picture of Oswald with the rifle (as well as the pistol he would use to murder Tippett) in their back yard earlier in the year. Conspiracy theorists sometimes allege that the photo was doctored but Marina admitted to taking it and several different groups of experts have examined the negatives and concluded that ti was not faked. (Conspiracy theorists often find it improbably that Oswald would have a picture taken of himself with a planned murder weapon. But the photo was taken in IIRC March and Kennedy's trip to Dallas had not been planned, much less announced, yet). We also know that the photo is genuine because Oswald gave a copy of it to a friend and wrote on the back "Killer of Fascists, Hahaha" in Russian. The handwriting has been shown to be Oswald's. When Oswald went into work that morning he got a ride from a colleague. Oswald had a long thin package wrapped in paper with him. The package was of such a size as could have contained the rifle. Oswald told his coworker that it contained "curtain rods" for his rooming house. The paper that the package was wrapped in was found on the sixth floor, but no curtain rods were ever found. Nor was anything else found that could have been in the package other than the rifle. Immediately after the shooting, Oswald fled the TSBD. He told the cops that he left because he assumed that work would close down after the shooting, but his had fled the building within minutes, a suspiciously short time frame, managing to get out just before cops locked down the building. He was also the only employee to flee the scene. This is why DPD Officer Tippett stopped Oswald. He matched a description of a man who had fled the scene where the cops believed the shots to have come from (based on witness testimony and the discovery of the gun).
So we know that Oswald owned the rifle which killed Kennedy. We can strongly surmise that he brought it to work that day. Oswald was the only person seen on the floor from where the shots came and his fingerprints were found at the crime scene. He was not seen anywhere else during the shooting (no alibi) and demonstrated consciousness of guilt by fleeing the scene and then murdering a cop when they tried to question him.