It reportedly is part of the “Paul is dead” hoax/practical joke which the Beatles supposedly worked into a number of their songs.
Of course Paul was never dead… and none of the Beatles ever admitted that they had engineered any sort of hoax or practical joke. The insisted it was just a lot of fans with a wild imaginiation.
SPECIFICALLY ABOUT YOUR QUESTION:
“Come together over me” is supposed to mean the three remaining lads visit the grave of the real Paul McCartney – now being impersonated by Billy Shears --(from Sgt Pepper).
“One and one and one is three” means – only three of the original lads are left.
“He wear no shoeshine” indicates he was buried in some taditional fashion which dictated the corpse shoulsd not wear shoes. (Have no idea if any such tradition ever existed) However in the picture on the front of the Beatles - Abbey Road album, the four lads are crossing the street …
Paul is dressed in white … the eastern symbol for mourning the dead …and Paul is not wearing shoes. (Who the hell cares … the music was great)
“Ju Ju eyeballs” refers to shining eyes … because coins would be placed on the eyes of the dead as a symbol of good luck in some English families.
It really was a lot of fun back in the '70’s, because everyone was always trying to find clues in Beatle songs for the Paul is dead hoax.
It also sold a lot of Beatle albums which were already considered old by most standards … because people wanted to listen closely to songs, play records backwards on their record players (remember record players?) and listen for “clues”…
“And here’s another clue for you all … the Walrus was Paul…” can’t remember which song that was from.
Oh well… That was then and this is now and it’s no joke … two of the boys really are gone. What a shame.