|Let me get this straight. You are looking for two individuals that struggle to create their happiness as a couple? I'm looking at your lists. You've sure read a lot of yaoi. Cool.
Kimi ni todoke They are obviously interested in one another, but due to shyness can't spit it out.
Spoiler (mouse over to view)
They eventually get together, but that's not the finale. I stopped reading by that point, but there are possibly major misunderstandings and obstacles standing in their way. Also, the two go on "dates" before becoming a couple.
W-Juliet. Classic. Reading the summary explains it enough.They have eyes for no one else.
Superior † Reading the prequel is recommended.
RomeoxJuliet You know, being based on the Romeo and Juliet.
Skip Beat and The WallFlower can count. In that case, I should mention Hot Blooded Woman. It does have a bit of class issue, but that appears later in this manhwa.
Warau Kanoko-sama and its sequel.
Othello about a girl with a split personality. It's a gag manga in my opinion. But the main personality has a crush on a guy and he seems interested in her.
I'll edit this post once I find some more.