Disclaimer - my work tends to be closer to 65k, and I don't write a lot of fluff (I tend to cut things that don't work in the first draft because the story doesn't feel right), so I don't have the same sort of task as it sounds like you will.
I do a lot of the same things Icehawk does. The one big addition is probably that I mark things that I feel need changing as I'm drafting. For the story I've done round one of edits on, I still have a list of minor notes that I want to work into the story.
I like setting things aside for a while, then coming back and reading through the whole thing again. Sometimes I notice that a storyline needs tweaking or that there are some major things that need to be tweaked or altered to line up smoothly because I changed the direction of the storyline halfway through.
I don't print out copies. I do highlight, take notes on a separate document, or in-document if necessary. For the piece I'm currently editing, because I'm reshuffling a bunch of things, I've added in reading through the chapter I'm about to start editing first, then taking notes on things that need alteration, then starting in on the edit work.
I keep track of my plot arcs mentally, so there are a lot of observations going on in my head about storylines and whether or not a good balance is being made. I look to balance out a story and make certain that certain arcs have enough time and balance, and then sometimes I'll set out to fix a problem like a character not having enough mentions in the story, despite the fact that they should be in specific scenes. (I have a ghost in Mahala. Only my narrator can see her, and in round one of drafting I was much more focused on the main line of events than all of the mentions of the ghost that really needed to be there.)
I tend to spend most of the second draft working on the huge, sweeping storyline changes, and then add in what I consider finer details down the line. Adding in descriptions, making sure I don't just have talking heads is important, but it's less important to the story arc, so that's somewhere I tend to slack off because I have to put a lot of effort into it and it's easier to do that once everything else is settled.