Hi again everyone. Sorry about my belated reply. The meeting with the priest went very well. He was able to lay some issues at rest and at least give me something to think about concerning others.
Mommie2Boys: I have had a few "dark nights of the soul" in the past, although this is by far the worst I have experienced. Your words ring true for me. The logical sense of the Catholic worldview is what ultimately caused me to convert a few years ago. Recently however I have read a lot of atheist arguments which made more sense to me than they ever had before. However, my meeting with the priest helped me to see that godless logic is not quite as airtight as many atheists claim.
Revan: Lots of my doubts were caused by militant atheists with a scientific background such as Richard Dawkins. However, their dismissal of miracles (e.g. Fatima) now seems a little simplistic to me. Thanks for the links, very interesting.
Marylou: This also seems like a very good and relevant read. Thanks for the link. I'll read it in depth when I have a little more time, as I am currently very busy with university work.
McMaster: I actually feel as if I am going to come out of this conflict with a deeper understanding and appreciation of my faith than before, since I have been forced to scrutinise it.
The historical aspects of the faith I was having most difficulty with were the creation account and other events depicted in Genesis and the existence of Jesus Christ, as many have argued there is comparitively little evidence for His historical existence next to other important historical figures. These doubts have been largely resolved. However, when I have a little more time, I will post the specifics on the Apologetics forum to hear the perspectives of Catholics on here.
GrumpyTroll: You were pretty spot-on with your analysis. Evolution is at the root of my doubts, as well as the age of the universe and earth. The priest I spoke to referred me to another priest who has a Ph.D. in Physics from Oxford University (he obviously doesn't think science and religion are at odds) and I will hopefully be meeting with him soon.
Philomena, miss fluffy, actiofidei and RoseofLima: Thank you very much for your kind words and prayers. They are truly appreciated.
So, in conclusion, my doubts have not been completely diminished, but they seem to be on their way.