Congratulations on a wise purchase. The series two MDA chassis is one of the best spaceframes out there. Probably on a par with, maybe superior to the Southern GT in some aspects. One of my friends has a Southern GT and he recently did a lap of Goodwood in 88s and that is fast. So you will have a wonderful car in the end. MDA's tend to operate under the radar of publicity on the GT40's site, generally due to Mark Sibley keeping a low profile but the products are excellent.
I never bought brakes when I got the car, so I don't have a spare set. There are lot's of options though.
If you need advise or feel you need to see the car, you are more than welcome. I don't know what experience you have of building cars, but the GT40 isn't easy.