Hey moops, I can completely relate to what you are talking about with mood swings affecting your relationship. I was going through a similar thing with my partner ~ 1 month ago. I've been feeling better about our relationship lately, but around Feb. I started feeling mildly anxious and depressed for apparently no reason, and to have a lot of doubt and unhappiness about my relationship sometimes even though nothing had changed and I have a loving and supportive partner. While I can't tell you why you are feeling the way you are, I recently began seeing a therapist and that has helped me to sort out what may have been going on with me, so I can share that with you and maybe you will see something relevant to your own experiences.
One thing for me is, I have a history of depression (I also had what you might call a "difficult" past). Even though it is not as severe as when I was a child and teenager, it still manifests itself for me in other ways--anxiety, indecisiveness, difficulty concentrating and focusing, loss of interest and enjoyment in things that usually bring me pleasure. It was difficult for me to recognize that even though I'm not suicidal anymore, these things are also symptoms of depression, and that they continue to impact my life and relationships. If you are experiencing something like that, especially if you have a history of depression or similar problems, you might want to speak to someone qualified to assess what's going on and help you deal with it.
Another thing that may be contributing is all the stress of med school applications. I was way stressed out around the beginning of this year trying to finish up my graduation reqs and write my thesis, study for the MCAT, and prepare to apply to med school. All the stress contributed greatly to my feeling depressed for "no reason", which in turn made me feel dissatisfied with my life in general and particularly my relationship, as I focused my unhappiness on the closest target. Since realizing just how stressed I was about all this, I've tried to take the pressure off some, which has helped a lot. My partner and I just got back from a vacation, and I have been giving serious consideration to postponing my application for a year to give me more time to get everything done as well as for travel and volunteer work. I think I will probably do this, as jut thinking about it has made me so much more relaxed and happy. Maybe that's not an option for you, but if you are feeling really stressed try to do something to relieve the pressure, especially something fun with your partner if you can.
Finally, you mentioned this woman is your fiancee--is that a fairly new thing? The reason I ask is because, my partner and I (while not engaged) have been together for a long time and moved in together ~5 months ago. While it has worked out great and I know it was a good decision, I have never lived with somebody I was romantically involved with before and I think it brought up some stress for me that came out as doubt about the relationship. It is normal when you make a big commitment to someone, be it marriage, engagement, or moving in together, to feel worry and doubt sometimes, especially in the beginning months; and for me, due to my depression and stress, this worry and doubt got a little out of hand for awhile. You might consider if that is a factor. It sounds like you really love this person and that nothing has changed between you two to provoke this worry and doubt on your part. It also sounds like you have some soul-searching to do, like I did, to determine if what you're feeling has to do with real concerns about the relationship or if it is related to issues you are facing in your own life. If it is not genuine doubt about the relationship but is coming from other issues you may be facing, then you owe it to yourself and your partner to figure out what those issues are and how to deal with them. I think it is important to be honest with your fiancee during this time about what you're feeling, but don't overburden her with your doubts and concerns until you have determined what they're really about. Sorry for the long post, and I wish you good luck in your relationship and in life.