Misc cleanup after complete read through

@mamund Please review and merge. I have regenerated all the files with the included script. There are a few sections with leftover [TK] etc that you would be best to address.

The following PR:
* Fixes misc typos, adds spaces, punctuation, etc.
* Makes some phrases into sentences for better readability and fixes grammar.
* Makes samples more readable (per input from @steveklabnik).
* Highlights as suggested change to a few sections (I add comments in the PR to point them out).