Any yoais where one of the guys is homophobic than gets into a gay relationship.

Hmm...
Koisuru boukun, but you probably already know that one ^^

Bl Motel...?

http://www.mangago.me/tag/homophobic

Was he homophobic at first ?
I don't remember ?... (￣∇￣")

What lies at the end

Story 1 of this falls into that category I think:

http://www.mangago.me/read-manga/abarenbou_kareshi/