The resevoirs on your pedals are your master cylinders. Sounds like you are talking about the bleeders on your calipers. If they look like tiny hose barbs they are the bleaders. Between the bleeders there should be a threaded hole with a sticker over it or a plug in it, that is where the brake line goes in. If they are the porsche style calipers that come with most VW disc kits they are a metric thread. If the calipers are Wilwood or something similar they are likely a standard 1/8" NPT thread. NPT is "national pipe thread". NPT is a tapered thread getting smaller the deeper it goes into the part. The clutch essentially hooks up just like a brake line. Solid line from the clutch pedal master cylinder to the transmission. From there you must use a hose to connect the solid line to the slave cylinder, since it will have movement. The slave has a bleeder on it also just like the calipers. The pedals should all be mounted where they are comfortable to you. Always use a plate under the pedals that is attached to the frame. Attaching directly to an aluminum floor in my opinion is asking for trouble. Here is a pic of my pedal assembly from my last rail. I had hoses from the master cylinder to the hard lines because my pedals were adjustable.
Anywhere there is movement use a hose. From the frame to the calipers or from the frame to the rear trailing arms use hose. I like to use a short hose on my rear calipers also so I can remove the caliper to change pads without taking the hard line loose, a lesson I learned on the last one. If you have disc on the back use a 2# residual pressure valve, if you have drum use the 10#. Somewhere in the front lines should be a proportioning valve if you want to adjust the front brakes. If you have tailights don't forget the brake light switch. Plan ahead, draw everything out and have someone check it before you waiste a bunch of time and money.
