I am a service advisor at a BMW dealership so I have access to full shop. So having a lift and certain tools may make things easier but not all required. And your current mods may make this job easier. Like sound tube delete gives you immediate access to the top of the line. And not having any cats gives you more room to work on the bottom. I don't have either. So for me, all the time was taken up by wedging my arm between the tunnel and trans to put the bottom of the line in the elbow.
Things you will need: 1 bottle of Ford Dot 3 of High Performance brake fluid, (or whatever fluid you run) long handle pick, long handle curved needle nose pliers, Teflon tape, mitivac vacuum bleeder or equivalent, #10.5 or #11 rubber stopper, 1/4" barb vacuum line connector, foam window cleaner, brake clean and beer of choice.
Here's what I did:
1. Disconnected the line from the top using a long handle hook pick, this will help you save the clip from falling into the wheel well and saving you hours trying to find it. Try to avoid pulling it all the way out if you can help it. You CANNOT lose these clips. Have some good absorbing rags under it as some fluid will leak out. Leave the reservoir cap ON or more will leak out than necessary.
2. Next raise the car up. Or put it on jack stands to give you access to the driver side. This is where not having cats would help. Look straight up by the bell housing. You will see a plastic elbow stuck in the side of it. The bottom of the line is stuck straight down into the elbow. Remove the clip on the top, again, try to avoid pulling it out all the way so you don't lose it. This is where long handle tools come in handy as I could imagine how little room you may have if you have cats. Long handle pick and curved needle nose pliers will be your friend. Use the long pliers to pop the line out if you can't get your arm up there. More fluid will come out so watch your eyes and mouth.
3. Remove the line from the top. Depending on the line you got, you may have to put the fittings in the new line. It was recommended to me to use a little Teflon tape on the fittings. Screw in by hand then snug tight using two, line wrenches if you have them. Spray a little lube on each end (like foam window cleaner) this will keep the o-ring from getting damaged putting the lines back in easier. Plug top in first. I found it best to run line under the master cylinder, then up over bank 1 valve cover along the black line already clipped on the valve cover, away from the headers. Then back down the center of the firewall down the trans bell housing to the elbow.
4. Raise the car back up, or climb under, whatever your situation is. Now this is the tricky part. Depending on if you have cats or not it may be a bitch. I simply had to wedge my arm up there and fight the line with one hand till I got it lined up just right to slide back in the elbow and push the clip back in. This is where not pulling the clip all the way out will save you a lot of time fighting this step in such a tight space. If you can't get your arm up there those long curved needle nose pliers may come in handy again.
5. Once you get done cursing at the bottom of the line and it's in there, lower the car smoke'em if you got'em, drink a beer, or do what ever you do to relax, the hard part is done.
Now the easy part. Some will say you don't need to it this way due to the system is self bleeding. But Ford uses a vacuum bleeder to bleed the clutch. To me if Ford took the time to write it up a certain way in their repair instructions why not just follow the recommended procedure and make it right and easier on yourself, with less margin for error? The parts are cheap and easy to obtain. You can get a cheap vacuum bleeder from an auto parts store or Harbor Freight if you don't already have one. The rubber stopper and barb fitting from Ace hardware for a few bucks. This is essentially making Ford's specialty tool for bleeding the clutch.
6. Top off the reservoir with whatever fluid you use, or the Ford HP Dot 3 if running stock, to the max line. Drill a hole in the center all of the way through rubber stopper to fit the barb fitting in it. Plug the vacuum bleeder to the other end. With the cap off, place the bottom of the rubber stopper directly over the reservoir. It won't fit inside it, it will just sit on top. Holding it steady pump the vacuum bleeder to 20inhg. Let it hold for 1 minute. If it isn't holding vacuum check for leaks, make sure the rubber stopper is completely covering the reservoir and that both ends of the line are secure. (Putting the system under vacuum is another good reason to do it this way to ensure there are no leaks) After 1 minute release vacuum put the cap back on. Hop in the car and pump the clutch 10-15 times. You may have to pick the clutch off the floor this go around. Then top off the reservoir again and repeat those steps at least two more times or until you get desired pedal feel back. It worked like a charm for me and, was great by the third time but, I did it once for personal reassurance. When you're all done zip tie the line to the black line going over the valve cover to keep it out of way of the header. Do it in two places a few inches from each other so the SS line doesn't chafe the black rubber line. Then go for a test drive. Get the motor nice an hot. You should notice a much more consistent pedal feel all the way through the RPM range. No increased pedal pressure for lack of fluid pressure going to the slave. Which I believe was causing my problem and most likely yours. If you find yourself boiling your fluid at the track. Go to a fluid with a higher wet and dry boiling point. The fluid takes on moisture over time so take note especially to its wet boiling point which will be it's weakest link. So FLUSH often for track use! Remember your clutch and brakes share the same fluid and master cylinder.
If you have any other questions hit me up. I would be happy to help.
