How many eps did Gilligan clear out from the rest of the Castaways and move to a different part of the island? Count the one where Skipper goes with him.

When Gilligan thought he was a vampire in the ep:Up at Bat.After a magic trick that didn't work out,Gilligan overheard the others saying mean things about him,he hurt so much that he lived by himself in a cave for a while in the ep:It's Magic!When he became bald in the ep:Hair Now,Gone Tommorow.When everybody was allergic to him in the ep:Allergy Time.

2 more possibilities:
Court-Martial
When the Skipper is accused of negligence in the marooning of the castaways a reenactment of the shipwreck reveals Gilligan was to blame as well so both move to the other side of the island.
Gilligan’s Personal Magnetism
During a game of bowling Gilligan, using a rock for a bowling ball, is struck by lightning and the ball becomes stuck to his hand through magnetism. Another lightning strike removes the ball but renders him invisible. The Skipper finds a note from him saying he’s moved to the other side of the island.
OK. This one’s iffy. :)

Another comes to mind.
Feed the Kitty
After the lion looks at the other castaways as different animals, they get a little nervous so Gilligan goes to the other side of the island rather than see his friend caged.

I'd add three "almosts" to this list: times when Gilligan seriously contemplated leaving, but ended up changing his mind.

Water, Water Everywhere: Gilligan is writing a farewell note that says "maybe everybody would be better off without me," but doesn't seem suicidal, as his poor friends later believe. Maybe he adds "I'm moving to the other side of the island" to his future notes so he won't scare his friends again!

Gilligan's Personal Magnetism: The Skipper finds a farewell note from Gilligan that says he doesn't want to inconvenience everyone with his invisibility. When the Skipper reads the note out loud, we learn that Gilligan was listening all the time. I rather think that Gilligan truly did intend to leave, and simply had not yet done so. It's hard to believe that he would write a false note and deliberately trick his friends in such a cruel way.

High Man on the Totem Pole: Gilligan intends to leave because he fears he will become a headhunter like his so-called ancestors, but the Professor manages to cure him of his fears.

I find it somewhat ironic that the Skipper fears Gilligan could not survive on his own in the jungle, especially at night. Why not? He seems to do a pretty good job of it on several occasions.

Oops! The middle one was already mentioned. You're right; it's iffy.