I would highly recommend reading it with the family trees of the major houses pulled up on a computer in front of you while you read. Likewise the maps. One of the initial things that can be baffling is the ever shifting geography of Middle-Earth - especially over the course of the creation stage and through the First Age. Tolkien is constantly dropping names of rivers, hills, mountains, forests, regions, etc. Having a good map is vital. If you're going all in for a thesis, it's well worth the investment to get a copy of "The Atlas of Middle-Earth"by Karen Wynn Fonstad.