<p>I'm trying to squeeze a little better quality out of my time lapses generated by OctoPrint.</p>

<p>I'm using the Raspberry Pi Camera Module V2 with a Pi 3. I've already edited the Octopi config to get 720p resolution, but the encoding during time lapse rendering is horrific. Blocky as hell.</p>

<p>Right now the encoding is set up at 5000k.
What am I doing wrong here?</p>

The resources you have at your fingertips are going to be more up-to-date than anything you'll find in a paper/published book. Use this amazing thing called the internet and read everything you can find. Use Google or your favorite search engine using appropriate terms. I'd suggest, based on your overly broad question, that you use "build your own 3d printer" as a starting point.
You'll find that
Instructables
is one useful resource as well as
MakerShed
for additional material. You will find a very large source of helpful information at
3dprintboard.com
simply by reading others' posts there and at other forums as well.
There is quite a bit to absorb and understand but with the internet at your fingertips, you won't be lacking for information.