This is a tall order. You're right in saying they will contradict each other.
This is true, there is no canon, and until recently the novels were mostly stand alone. There are some classic novels that don't fit in to later canon that you should probably read ("Spock's World" and so forth), but a chronological list of every media? I don't think it would be very pretty.
I've not read a ton of the novels. Personally, I like/own the Crucible series by David R. George III. Taking only the shows and movies as canon, he explores how the events of "City on the Edge of Forever" affected each of the Big Three. Spock's is a pretty straightforward story, while McCoy's is mostly told from the alternate reality where the Nazi's win WW2. Kirk's is kind of weird, mostly him reliving experiences in the Nexus if I remember correctly.