Hi oakwood,
As I'm the one reading the works of Josephus for the database project, I should be able to fill you in about the details of his writing.
For starters, I will give you an insight about in which order I'm reading his works: I started off with his autobiographical notes. I then read Wars of the Jews mainly because Josephus took an active part in them, so he's an eye witness of sorts with a strong subjective and partisan view. At the moment I'm reading his Antiquities of the Jews and I am in Book VII currently, which isn't nearly half way through that work as of yet. So far it consists mainly of a Reader's Digest type of retelling Biblical History with quite a lot of personal, Pharisaical slant on things. That leaves Against Apion to be my last read some time in the future.
Here are a few websites/pages about him and his works which I found quite helpful:
_http://en.wikipedia.org/wiki/Josephus
_http://www.josephus.org/home.htm
_http://www.livius.org/jo-jz/josephus/josephus.htm
During my reading I made several remarks on different threads, the most important of which I will list here for you to get some further background and to provide some inkling on the problematical sides of his works that I've encountered so far:
http://cassiopaea.org/forum/index.php/topic,31732.msg487423.html#msg487423
http://cassiopaea.org/forum/index.php/topic,31732.msg483551.html#msg483551
http://cassiopaea.org/forum/index.php/topic,33985.msg475828.html#msg475828
http://cassiopaea.org/forum/index.php/topic,33985.msg487417.html#msg487417
http://cassiopaea.org/forum/index.php/topic,33985.msg489781.html#msg489781
http://cassiopaea.org/forum/index.php/topic,33985.msg489799.html#msg489799
http://cassiopaea.org/forum/index.php/topic,33985.msg487417.html#msg487417
http://cassiopaea.org/forum/index.php/topic,33985.msg496485.html#msg496485
http://cassiopaea.org/forum/index.php/topic,33985.msg498071.html#msg498071
As for the extent to which his works are in any way distorted I would like to pass judgment for the time being. We might discuss that later on after you've read his works. I don't want to introduce or reinforce any preliminary bias either way before you start reading. Just try to keep an open mind and see for yourself, but always remember the position Josephus found himself in when he started writing, who his patrons were and why they were supporting him in his endeavors. Take into consideration also who his targeted audience/readership was.
I hope this is enough to help you on your way. If not, just ask. :)