When I was working on my senior project for my undergrad (which was obviously not nearly as frightening a thing as a master's thesis), there were two related things that helped me immeasurably in getting through my rough draft. One, like NerdGirl said, was to take baby steps. The other was to let go of my perfectionism.
I had a rule that I had to write 400 words a day, six days a week, until I got to the end. Each day, no matter what, I would sit down with my outline and pick a sub-point that I felt like I was ready to write, and I was not allowed to leave my chair until I'd written 400 words. Occasionally I would get on a roll and churn out 600 or 800 words, but usually I'd quit at about 450. Then I would go eat a handful of marshmallows or something as a reward for accomplishing my goal.
(One of my roommates had a completely different strategy that worked well for her: One day a week was senior project day, and she would gather up all her materials and be in the library for 10 straight hours and come home with 10 or 15 pages written. I ... do not have the attention span for that, but it worked for her, anyway.)
I was also very clear with myself that they did not have to be 400 GOOD words: no pressure to get it right the first time. I just had to get the ideas onto the page; clarifying and making things pretty could come later. Occasionally if I was really stuck, I would give up on academic language altogether and write like I was explaining the point to a friend: "Okay, so, most female characters are supposed to be all angelic and stuff, right? But Mr. Rochester likes to think of Jane as a fairy instead of as an angel, and that's part of why she ... " When I got to the revising stage, of course, it was a headache trying to sort that out, but less of a headache than starting from scratch because at least the ideas were on the page.
Good luck with your thesis, Whistler! Keep us up to date on how it's going.
