As Photolar points out, there are two holes in the bottom of the master cylinder. One is fairly large and causes no problem. The other one is so small, that you will not spot it, if it is clogged, and you really have to look carefully. I use a hair from my steel brush to make it free all the way trough. This is normaly the most common problem when it comes to bleeding, it is not possible to bleed unless this is in order.
The piceses in your photo is displayed in the correct order. The cup in the end goes with the dome into the spring. Inside the dome there is rubber, so when you press the brake handle, it lets the fluid pass the rubber in the dom, but stops it from flushing back.
When you are doing your brakes, do it all the way trough. Take the caliper off, rinse it, clean out the groove for the square piston seal properly, install a new piston seal and check the piston itself. Chipped off chrome on the piston wall will damage the seal and fluid will eventually seep out. Clean pipe the connects to the caliper, the hoses and the joint in between. I use compressed air and sometimes a piece of stee wire comes in handy. Old rubber hoses get soft and will expand when you brake and you will have poor brakes.
Something to read here:
http://www.hondahobby.no/website.aspx?displayid=1610