Curate, connect, and discover
I have been rewatching some Bob's Burgers episodes and now I am going to show my headcanon of when Zeke first came to Wagstaff. TLDR version, I think Zeke became a student at Wagstaff between 4th and 7th grade. I think my safe bet is either 5th or 6th grade unless I find more evidence. Here's the evidence of how I came to the conclusion. So we know that Zeke wasn't there when Tina, Jocelyn, and Jimmy Jr. were in third grade because in the episode, "Can't Buy Me Math" Jocelyn immediately reveals that she remembers "the pee thing" while neither Zeke nor Tammy comment on it (Also wanted to bring up I know Darryl said 2nd grade but keep in mind he's a grade lower than Tina and the rest). Tammy doesn't because she wasn't there when it happened because she became a Wagstaff student in 8th grade. Jimmy Jr. left before we could ever find out if he remembered. Tammy and Zeke would have definitely commented on remembering it if they knew about it, one being more malicious about it than the other mind you.
So to me, I think it's safe to say that Zeke wasn't with them during third grade. I don't think Zeke was in Wagstaff in 4th grade either because in the episode, "A Fish Called Tina" We get a flashback of 9-year-old Tina with other students. Jimmy Jr. and Jocelyn are in the flashback, but not Zeke. Lastly, in the episode, "A Few Gurt Men" it is revealed by Mr. Branca that someone tried to flush down three spoons last year, which Zeke apologized for. So it's safe to say Zeke was with them during 7th grade and didn't just recently transfer to Wagstaff in the 8th grade like Tammy. So because of the evidence I gathered so far, I think between 4th and 7th grade is when Zeke moved and became a student at Wagstaff.
My guess is 5th or 6th grade until I see something that contradicts it.