No. You don't need the brake master cylinder, your old one will bolt up to the manual pedal tree. You will need some brake line pipes to finish the hydrolic lines for the clutch. You should be able to pick those up at autozone.
The other thing that you need is the hasport auto-manual tranny mount. The actual mount bracket (part welded onto the frame rail) on a manual is pointed upwards, where the auto bracket is just straight horizontal. This causes a 3 inch or so diffrence in mounting locations. The hasport conversion mount corrects this.
Then when you mount the linkages, your going to have to drill 2 holes for the stablizer rod bolts. Finally, since the auto gear selector box is gone, your going to be left with a rather large hole in the floor/center tunnel. You can either weld in a peice of medal, or you can do the lazy way that I did when I did the swap is get an aluminum sheet from homedepot, cut to fit, then use some sealant caulk to glue it in place and keep it water tight.
If you can find a manual civic in a junkyard you'd do better to pull teh lines off of that, since buying it from a store you're going to have to bend and route it, unless Autozone sells prebent application specific line.
well its not too bad for the clutch line since theres only like 4 bends in the entire thing. And if you have extra line and you don't feel like cutting and flareing it, you could make up the extra slack by putting tons of extra bends in it. Bending tubes are really easy to do also. Just take your time so you don't kink the tubes.