I go through first draft chapters in batches of three and identify bits that need changing. I used to do this with print-outs and highlighters (one colour each for delete, add, change [meaning keep the same idea but improve it] and redraft). It's much quicker on the Kindle, as well as saving tons of paper and ink.
After that I go through the chapters, again in batches of three, on the computer and make necessary changes. Often I'll leave something for later, and add it to a special to do list which I'll come back to after the entire chapter-by-chapter redrafting is done. Things included in that list are possible extra scenes and potential changes which have a serious impact on other parts of the book. Everything that's confined to just a single given chapter I'll change when redrafting it.
I'm redoing chapter 7 right now (almost done) and my end-of-redrafting to do list is already pretty long, which I'm quite happy about given my tendency towards brevity. I'm also considering whether or not to have an appendix (in Bane of Souls I had one containing the rules of Meier). I don't want one as padding, but there's some potential for extra bits that don't fit the story but would still be interesting.
Once the first redraft is entirely done that almost certainly won't be the end of the matter. Bane of Souls underwent four full redrafts, and I expect a similar number will be needed for Journey to Altmortis. Rejigging chapters and perspectives so that the story flows well, nailing especially important scenes and ensuring characters are consistent throughout will take a little while.
It's also a bit tricky to make sure characters follow on from the previous book (well, those who were in it) whilst taking account of the very different nature of the Altmortis story. Fritigern and Athanaric graduate from being minor characters to major ones, and likewise Roger the Goat (probably the most fun character to write).
Hmm. For a writer who keeps banging on about how brief he is this entry was longer than I anticipated. Anyway, I hope that people who bought Bane of Souls and liked it enough to come visit this blog found it interesting.