With the hydraulic throw out bearing mounted to the trans with the braided lines exiting the scattershield at the clutch fork hole all that was left was the clutch master cylinder install. The difficulties of mounting the master cylinder quickly presented themselves. I now saw why the aftermarket kits would not work with my setup. The problem is that my after market brake booster setup was right there. In the same area are the wiring harnesses, brake lines, etc... Basically you want the master cylinder push rod to mount to the clutch pedal arm as close to the pivot point as possible. The trick to any lever system is in the leverage.  
  You can see by the pic of the installed master cylinder that there really weren't that many options. We cut 2 pieces of 1/2" thick aluminum and made a plate for each side of the firewall to strengthen it. The master cylinder push rod and mounting bolts go through these plates. At first the distance from the clutch pedal arm to the push rod location was a concern. However, we quickly realized it was gonna be close.  
  Using a hydraulic throw out bearing requires a pedal stop. If you do not use a pedal stop you will apply to much pressure to the bearing piston and blow the seal. The clutch master cylinder pushrod only needs to travel 1 inch. After taking some measurements we made our trip to the coffee house for another R&D session. We came up with a fairly simple yet effective design. It would have a piece of angle welded to the clutch pedal arm. To this piece of angle we welded a 1/2" nut. We then screwed a 1/2" bolt through the nut using jam nuts at both ends (the head of the bolt would face toward the firewall). We then welded a flat plate and a piece of angle to the pedal housing. To that piece of angle I bolted a square poly-urethane suspension bump stop. Now I had a rugged, silent, adjustable bump stop. Just loosen the jam nuts and screw the bolt in or out as needed to adjust.  
   
       
The pedal stop also provided the distance needed to make a connection to the master cylinder pushrod. I welded another piece of angle to the one housing the bolt so that I would have a flat side facing mounting point. I used a spherical rod end on the end of the push rod and bolted this to the piece of angle. It works perfectly.
After burning up a clutch line (my fault, moved the line positioning when doing my electrical project) I decided to make a custom bulkhead. This way, if a line ever got damaged I would not have to pull the trans to replace it. I went through about 3 variations before finally going with this one. Now I have 2 lines from the hydraulic TO bearing going to the bulkhead plate, then 2 more line going from the bulkhead plate to the clutch master cylinder and the external bleed port. The bulkhead plate was made from a couple pieces of scrap steal I had. I welded them together at the angles I measured for, then drilled holes to mount the 2 90º adapters (for the lines to attach to) and 2 mounting holes to bolt to the scattershield (I had previously drilled, tapped, and heli coiled the scattershield).