Put yourself in Johnson's shoes in the weeks and months after the shooting. Bits and pieces come out that Oswald was paid...that it may have well come from Cuba...that Kennedy and the CIA had tried to kill Castro...and that Castro simply got smart did the whack job on Kennedy. If all the pieces fall down correctly...how do you punish Castro or Cuba...total invasion? It starts to smell like the episode that started World War I. When Austria spoke its words to invade the Balkans to punish them for the death of the young prince...it rippled all across the globe. Johnson probably added up the numbers and looked at history in the making...and told the Warren commission and the FBI to screw this investigation up as much as possible. You simply can't tell the story.
As for the pieces left on the table from this report. What became of the cash that Oswald took possession of? Did his wife take it and hide it? Did the FBI recover it and just burn it? Was Ruby part of the same group, and simply there to clean up the mess at the end (he might have terminated Oswald if the Dallas cops had not been so quick to locate Oswald)? Were Cuban or KGB marksmen on location to take the other shots, thus allowing Oswald to "think" he did the deed? Did the Dallas cops never figure out this angle or was it simply way too complicated for them to understand? To know the schedule of Kennedy...would Castro simply have turned to the KGB and asked where Kennedy would be in a month or two...which they would have likely known?
Alot of question are left to be answered. But you start to understand the absolute mentality of the administrations since 1963 on maintaining the embargo against Cuba. There are lots of reasons to terminate it...even Jimmy Carter hinted that before...but none of them will lift it...not even Clinton would do that. There is likely an absolute stand on Castro...to wait the guy out.