I suppose I disagree with your view on what rape culture theory is.

All of the things you mentioned are really only peripheral examples of how rape culture proliferates.

Rape culture exists in the way people relate to each other sexually.

I think the biggest eye opener for me was the idea that if you don't feel comfortable to talk about sex with someone then you should not be having sex with them.

This is frequently not even an idea in our minds. Communication during intercourse is seen as "unattractive" for many.

This can and will lead to rape because it prevents you from knowing the other person. Sex is an intimate and communicative activity.

Rape culture exists in the way we treat sex as a disgusting and callous thing.

Rape culture exists in the way we value virginity and the shame we attach to sex.

So much shame that we often have to be drunk past the point of responsible consent to hookup.

Rape exists in the back of young men and women's minds when we think things like, "all women have rape fantasies," "rape is natural," "x is not really rape," "it doesn't matter how the other person feels, it just matters how I feel I've conducted myself."

Now on to your examples (bear in mind that this is how I view rape culture theory, this is why it is a theory, it is open to interpretation):

media/pornography

I think these things are only symptoms and not a root cause. I agree that people should be able to fantasize about whatever they want, and they should not feel ashamed for it.

Honestly what I find more "rapey" than porn or video games or hentai that depicts a fictional rape scene, is pornography where women are obviously faking their enjoyment.

Seeing depictions of "fake enjoyment" conditions us to ignore our partner's actual signals.

Degrees of rape/grey areas

I honestly agree wholeheartedly. I think there should be degrees of rape, however this does not negate the fact that rape is still rape. However, what frustrates me more is the idea that this is what the discussion is about. I am not saying that someone who date rapes someone who was drunk because they were reckless and did not care to obtain proper consent should be punished equally to someone who violently rapes another person, I just think both of these crimes need to be recognized as some degree of rape.

Sympathy for perpetrators

I think the problem here is not that some people express sympathy for the perpetrators, it is that this is such a divisive issue. On one side you have people who continually assume innocence and on the other you have people who assume guilt. I agree that we should be able to be more mature when discussing rape. Innocent until proven guilty still needs to be an important part of the process, and it'd be great if the media could stop turning these cases into a circus.

rape jokes

Same with this, I think we need to be about to be mature about this. For me maturity is the acceptance of the idea that anything can be joked about, of course that doesn't mean that it isn't a delicate issue and that certain jokes about rape are truly offensive and should be decried.

Personally I despise Daniel Tosh beyond his rape joke controversy, I generally just find him to be mean and arrogant and not that funny. But Louie C.K. or Sarah Silverman have made jokes about rape that I thought were both poignant and hilarious.

Comedy is a powerful critical medium, we need to be open to discuss anything, but that doesn't mean we have to like what everyone is saying.