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As mentioned back on the first page, you have a pair of twelve inch long 3/16" diameter lines, complete with fittings, that will need to be properly bent to fit between the master cylinder output ports and the proportioning valve. OK, so I'll confess that my bending is not something I am proud of, but like MikeW said, they work and who is going to be looking at them when the hood is closed? The master cylinder is divided into two sections (as are most) and the larger section (at the front of the master cylinder) needs to be connected to the combination valve port that feeds the front disc brakes. Want to play it safe, follow the lines coming out of the combination valve just to make sure you have the correct line identified. A single line goes to the rear axle while the two front calipers are connected via separate brake lines. I picked up an $8 tubing bender at the NAPA store which was worth the money. It would have been more beneficial if the bend radius had been smaller (which it easily could have been). Take your time and work on getting the steel lines to line up properly with the ports. We unbolted the canister that was on the fender because it was in the way while trying to test fit the lines. I tried to find a pair of 90 degree fittings which would have made the connections at the master cylinder much easier to do....but, no luck. Take your time and you will get it, even if it looks as bad as mine. At this time, do not connect the brake lines. We will get to that a little bit later.
Next, connect the 3/8" low pressure return line to the steering box, pump reservoir, and Hydroboost. The filter came with no hose clamps so I made a quick dash to the parts store to pick some up....all of my spare clamps were too big. The middle hose of the "T" connects to the power steering pump reservoir. The short leg connects to the low pressure return port on the steering gear box and the long leg connects to the low pressure return port on the hydraulic booster. Take a few minutes to properly determine the best position for the filter. You will find you are near the steering column shaft and you would not want things rubbing against each other as the steering wheel is turned. I cut the hose and inserted the filter (as seen above) and then trimmed a little more off the free end to get the hose to route where I wanted it. Just remember, measure twice, cut once....and you will be good to go.
The hoses on the hydraulic booster are next on the list. Of the remaining adapters, screw two of them into the "to power steering pump" port (the inlet connection) and also into the "to gear box" (the outlet connection) port. Then attach the hoses to the adapters. The fitting on the "to reservoir" port gets the last hose which is the long leg of the low pressure "T" return line. It is held in place with the supplied hose clamp.
I zip tied (better than duct tape!) the high pressure line (between the PS pump and the hydraulic booster) in place so as to keep it out of the way. In general, always pay attention to the way in which you route hoses and lines carrying fluids. You do not want them touching any rotating objects (fan blades, serpentine belt, pulleys, etc.) nor do you want them to abrade on any sharp corners.
One thing that I noticed was that the pedal rod (the part that connects to the brake pedal) is probably a little different in length than what you removed. No problem except that it will probably cause your brake lights to remain on even though you don't have the pedal depressed. Not a problem....the TJ has an adjustable brake light stop switch. If you look under the dash, the stop light switch is mounted on a bracket that sits in close proximity to the brake pedal. There is a spring loaded plunger on the switch that is actuated by the brake pedal when the brake pedal is at rest (no pressure on it). To adjust the switch plunger, first locate small pair of needle nose pliers. Push the pedal down slightly and carefully pull on the switch plunger with the pliers. It will take a little bit of force but it will slide forward. Let go of the pedal and as it returns to normal, it will push the switch plunger back into position and you will hear a little ratchet sound as it does. Congrats, you have just adjusted your brake light switch for your new pedal rod.