The View Askewniverse/WMG

Either the Happy Scrappy Hero Pup girl or the little girl Randal sells cigarettes to in Clerks is the same goth/emo/whatever chick who calls him a freak in Clerks II.
Why? Because it'd be funny as hell, and fit in well with abundance of Can't Get Away With Nuthin from the first film. The only flaw is that the goth chick doesn't appear to have been played by the same girl as either of the other two.

There are two separate people named Willam Black.
Just to recap: there's a skinny guy in Clerks named Willam Black who says "its beautiful, man". In Mallrats, the fat guy trying to see the sailboat is also named Willam Black. Kevin Smith supposedly claims they're the same person. But we can all agree they're brothers, cousins, or relatives with the same name. One source claims that one of them is named William Black.

Dogma was the reason why the Clerks cartoon was canceled.
Religious groups who hated Dogma forced ABC to buy the show only to cancel it and prevented all studios from buying it.

Don Wrigley has a sister who married a man with the last name Black, and she and her brother have similar ideas on sibling naming.
Granted, it makes the issue of why they went to different schools confusing. Perhaps there was a messy divorce and the kids took sides? There are more arguments for them being different people than for them being the same.

Nurse Graves from The Road to Wellville is one of Randal's ancestors.
She had a much younger brother, or possibly a young nephew, who traveled east and settled in New Jersey, married a racist and latently homosexual woman and started a family. One of their sons married a woman from the Bruce family, and Randal was born to them in 1972.

Jay has Asperger's
He's an atypical portrayal due to his laid back Stoner tendencies, but he exhibits a lack of understanding of social boundaries (especially with but not limited to the opposite sex), has absolutely no verbal filter, sometimes appears to struggle to process his environment, and demonstrates stereotyped and repetitive speech patterns and behavior. He also uses a number of atypical terms of his own invention which he seems to expect other people who have never met him before to understand, indicating a degree of mind-blindness.