1. If you don't have them, a set of Metric line wrenches are awesome. Basically they wrap about 3/4 of the way around the flare nut fitting so that you won't round off the fastener when you try to loosen the metal brake lines leading into the Master Cylinder. Sears has a set for $20-$30 it think.
2. When reinstalling the lines, it sometimes helps to leave the M/C a little loose on it's mounting bolts so that you can wiggle it a little to get the lines back in the holes dead on. If you feel any unusual resistance, STOP and try lining it up again. If you get it in there crooked, it will crossthread and leak.
3. After you install you will obviously have to bleed the brakes. If you don't bench bleed the M/C, it will be really hard to get the fluid going. It's not impossible though and there is the "stick trick" which is currently being discussed in the Yahoo diesel mercedes group. Basically you just put a big stick pushing all the way down on the pedal and leave it overnight, somehow it allows enough air out so you can bleed the brakes. I've never tried it but al lot a people swear it works for hard to bleed brakes.
4. While you have the system open why not check for hoses that need to be replaced? Also don't drive on this thing- I had one that would pump up but it blew out completely right when I needed to stop for a red light! Good thing no one way coming the other way. Of course this was in a 1962 VW crew cab with a single circuit M/C.
Don't forget to wash the brake fluid off your paint! Have fun.

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~Sugi
1983 300DT
1964 Triumph TR4 (back in the stable after 18 years- same car!)
2004 Pontiac Vibe
1986 Honda Elite CH250
1971 F100