Hi, I'm not all that experienced but I had my master cylinder on and off 3 or 4 times a couple months ago. It really is a piece of cake.
The cotter pin connecting the push rod to the pedal arm needs to be removed. Grasp it with a pair of snub-nose pliers and give it a sharp tug. A flat head screwdriver is helpful to bend the tang on re-installation.
My M/C had two hard brake lines - these get removed next. It's probably best to use a flare wrench on these to avoid stripping anything. Re-installation of the hard lines is a little tricky because they have to be square to get them started. Maybe try to start the nuts by hand to make sure they are not cross-threaded.
If you are having trouble getting the hard lines installed, you might want to connect the lines to the master cylinder before securing it to the frame. Or at least leave the two main bolts loose. This allows both parts to move and a little more freedom or wiggle room to get the nuts started.
You might have to bend the hard lines just a little bit, especially if the end-cap on the master cylinder was removed. If so, be careful not to crimp the lines.
Two bolts secure the master cylinder to the frame, and they thread into a single flat iron with two threaded holes. I found it easiest to use a tapered punch (pin) to line up the front hole (closest to the engine) while installing the bolt in the rear hole loosely. Then install the front bolt and tighten up everything.
The push rod gets adjusted so the pedal arm is 13/16" away from the toe-board / firewall. I used a piece of 1 x 2 as a 3/4" spacer (close enough I think).
Also, you might consider bench bleeding the master cylinder before installation. And for me, I found the "speed bleeder" valves handy for bleeding the brakes.
