One of the hardest things about independently guided research, in my experience, is that you rarely have someone to turn to for a second opinion. Of course your committee is there to help you with the big decisions, like if a possible case study will be productive or whether the project needs to go in a different direction. It's those little everyday things like "what to read first?" or "how should I allocate my time?" that you can't rely on your committee for--at least not regularly, if you want to live to see your defense.

It's really difficult, though, to make constant decisions about how to proceed with a large-scale scholarly study! Here are a few choices that you have to make on a regular basis:

Should you do primary source research first or read the secondary literature for context?
How should you prioritize your sources in order to examine the most important and relevant documents first?
Should your "freshest" hours--the ones where you have the most mental energy--be devoted to writing or to reading and note taking?
Should you continue editing this chapter to death or move onto the next chapter?
Should you give up or keep going?

I read this fascinating article in the New York Times Magazine a few years ago about decision fatigue. Experiments have shown that we humans get exhausted by making choices, and at some point every single day we hit our max quota of self control. We just don't want to make hard decisions anymore! We succumb to our urges, give up on our dissertations for the day, and get in bed to watch Gilmore Girls.

So here is some advice I have for minimizing those decisions and maximizing productivity during the document analysis phase (meaning, when you're reading and taking detailed notes on all those PDFs you OCRed and organized in your database).

It may be arbitrary, but choose a path you will take through your documents and then stick to it. At various points during my short research life, I have worked through my sources chronologically from when they were written, chronologically from when I collected them, by archive, by collection, and by box and folder they were stored in. Do not constantly reassess whether you are reading the most valuable materials first. The truth is, you don't yet know what's valuable. That's why you're reading through everything. Yes, sometimes this means you invest a lot of time taking notes on something that you later realize is meaningless, but just as frequently you end up taking notes on a gem that becomes the centerpiece of your argument.
It's hard to decide what details in the document you are analyzing are relevant. You don't want to waste time explicating information that does not support the argument you are building or the story you are trying to tell. To minimize those decisions, I constantly ask myself "what will I be looking for when I come back to these notes?" It's impossible to answer this question correctly 100% of the time, but I always try and capture the basic outline of events that relate to a larger, macro narrative. I would not waste time detailing the events of a small fight amongst a JCC Board of Directors, because those happen all the time. In all likelihood I won't include a paragraph in my dissertation about how they funded the construction of an elevator, so I can omit a note about that. If the small fight, however, is related to a larger fight happening among the Boards of the Jewish Federation or the Jewish Welfare Board, I will take copious notes on the debate. Remember, you can always list a few key words at the end to jog your memory should you one day be looking to write about that small fight that once looked irrelevant...
Always do the hardest mental work first. I'm a morning person, and so I try not to respond to email until I have worked on the dissertation for a few hours. You want to exercise that self control when you most need it, so don't save important tasks for later. You might become decision fatigued before it gets done! If writing is the hardest part of research for you, you do that first. If you struggle to focus on books, do not read the Facebook until after you read a few chapters. The Facebook will still be an easy read later.
Work somewhere that limits your choices. I like working in coffee shops because they do not have televisions and they do not let you clean their kitchens. These clearly are my two favorite forms of procrastination.
When a task starts to feel like a chore, move on. There's always more work to do. If you're frustrated or your attention is waning, you've already made the decision to quit. Try reading if you've been writing, or perhaps do the dishes for a while.
Eat a snack. Glucose helps combat decision fatigue for a few minutes. It's just long enough for you to convince yourself that you've got it all under control.
When you're done, you're done. Do not beat yourself up, do not feel guilty. Life is long and you cannot afford to retire until you're in your eighties, Millenial. The work will be there tomorrow. Researchers are mental athletes, and recovery time for the brain is equally as important as the workout.

Any other tips out there for avoiding research paralysis?