I feel as though there's a great divide in communication between the two of us, that we both want to be together but at the same time we end up bickering over misunderstandings way too much. I don't understand him and he doesn't understand me. I just wish there was a way for the two of us to be together and get a mutual understanding of one another. I also can't help but think it's mainly my fault for not trusting him and not wanting to (in his words not mine) "take a chance" on him, this is my first I guess...serious relationship and while we do have some great times together a lot of the time we both end up fustrated and annoyed.
ISFJ's help!
I'm not an ISFJ, but I might be able to help, as I'm in a relationship with one.
One thing that I've learned was that you need to take deep breaths when you notice yourself getting angry with him. ISFJ's are very loyal to their friends and mates, and the last thing they want to do is hurt you. In fact, they can sometimes be downright offended if you accuse them of trying to manipulate you...so don't do that.
Me and my SO bicker a lot over what turns out to be misunderstandings, too. If this is the case, stop and realize that what you're getting angry over could be a misunderstanding. Just try to stay calm. And even if you do end up bickering, don't dwell on it. Just let it go and kiss and make up, so to speak. If you guys spend enough time together, you'll get to know one another's quirks.
Also, ISFJ's do want you to trust them as they realize that trust is an essential part of a relationship. I honestly think NT's have trust issues, but you do need to try. Ask him to be patient with you, but you've got to show an honest effort, too. I'm sure if an ISFJ male had it his way, you'd leap into his arms and be butter.

But alas, NT's don't roll that way. It's just another thing you need to teach youself.