Hi Rich, this is a very good question.
While planet formation from a protoplanetary disc can be considered confirmed by recent discoveries of protoplanetary discs around other stars, there are no complete and detailed theories that would be proven accurate at this moment. This is as far as I know. I can easily be wrong of course. To get more details one would probably need to dive deep into the actual science papers.
Personally, I'm convinced that planets orbit inclination was caused by an early interaction between numerous planetesimals and protoplanets. Actual planet collisions in later times are unlikely but still possible.
Another interesting detail is solar system planets have very different rotational axis inclination. For instance, Venus have 177 degree axis inclination meaning it actually spins in the opposite direction to the Earth! Can you imagine how fierce and terrifying those early days of the solar system could be?
BTW, few years ago I had a good time playing games like
Super Planet Crash. That particular one probably isn't very precise, but quite educating nonetheless.