If you suggest something please leave a link and/or discription. Thanks.
What I want is one with one of the following:
-the uke is afraid to tell the seme he is gay

• the seme hangs around the uke a lot and can't take it anymore so he either leaves or makes a move
• the uke/seme has a fear of thunder/ lightning, the dark ect... Except I want the uke/seme to get afraid more than once or twice please
  -the uke tries to commit suicide(doesn't succeed), becomes A shut in, or he gets hurt because of the seme rejecting him(or it could be the uke rejects seme I don't care either way)
• one of the characters(uke or seme doesn't matter) goes to one of his other friends (who isn't gay) with his relationship problems consirning the other person
• uke/ seme gets really sick with a high fever
  -the uke/seme runs away from the other
  Any of these will do thank you
  Sorry to be so specific! 🙂

When life gives you lemons, squish them

Quote from Wolfy100

the uke is afraid to tell the seme he is gay

Kurayami ni Strobe
Rakuda Tsukai to Ouji no Yoru second story.
Pokerface (shonen-ai)
Kanashii Doubutsu
Tatsu no Otoshigo second story (shonen-ai and beautiful)

I don't know if all these will match your criteria though. For instance, in Rakuda it's not like he's afraid of coming out but rather, he doesn't want to admit to himself (or the seme) that he's capable of love.

Quote from Wolfy100

the seme hangs around the uke a lot (...) he either leaves or makes a move

Well. I want to say Kirai ja Nai Kedo the second couple in Warui Koto Shitai but his move may not be what you're looking for.

He blackmails the uke into playing with him

There's a more realistic reaction in Soredemo, Yasashii Koi o Suru but it's the uke who "makes the move" and not the seme. Sorry if it's not helpful.

Quote from Wolfy100

the uke/seme has a fear of thunder/ lightning, the dark ect...

Furueru Yoru no Himitsugoto
Kiss in Darkness

I don't remember how many times they had to suffer through their fear though. Maybe not enough for your liking.

Quote from Wolfy100

the uke tries to commit suicide(doesn't succeed), becomes A shut in

Under Grand Hotel (2013)

the uke doesn't become a shut-in because he's already in jail. Still, he clams up emotionally and tries to off himself multiple times.

Hikikomori without the suicide attempt:
Konbini-kun.
Nanadome no Gomenne (shonen-ai; incest)

Quote from Wolfy100

or he gets hurt because of the seme rejecting him

Boku no Shiru Anata no Hanashi first story
NightS last story Reply
Overdose
Udagawachou de Mattete yo. (kinda fits; gender bender)
Shiranai Kao first story

Some of these are uke rejecting seme and some deal with cheating and redemption. Some of these could fit in your other requests too, like Shiranai. Some stories named above also include rejection and people getting hurt left and right. Haha.

Quote from Wolfy100

one of the characters (...) goes to one of his other friends (who isn't gay)

I can't remember anything like this :'(

Quote from Wolfy100

uke/ seme gets really sick with a high fever

Haikei, Niisan-sama (shonen-ai and incest)
Sorenari ni Shinken nandesu.
Abiru Junjou
Saihate no Kimi e (I'm not too sure though)
Also this threat

It's the Art of Time, it's the Art of Life--
Of the player and the craftsman,
Of the writer of songs, of the creator of love,
Of those who will follow, of those who led,
There's no other way in the world ahead ♥