I agree that you can't let little things like your beloved not saying goodnight, or needing time to be in class, work, with family, friends, etc, get to you. LDR is a challenge, no doubt, but just as with any relationship, you have to be a couple but still grow as individuals and keep your interests, hobbies, and relationships with family and friends. As time goes on, you learn to find a balance.
In the end, the time apart and all the waiting is worth it, when you find THE ONE. And of course it is natural to say when you know, you know. We were engaged before we met face to face. We just knew. We've been married 9 years, have lived in the US, then the UK and now back in the US, but we have never regretted the time it took to finally be together, and because of visa processing, have even had to spend time apart married, just a month or two here and there. All worth it.
Even if you can't have a long visit, short ones here and there until you can have a lengthy one are worth it, because it gives you time together.