You're not going to mate the master cylinder up to the same position on the pedal as the stock clutch linkage. You will go higher up. This means taking the pedal out of the car and drilling a new hole. You will have the option of relocating the clutch pedal position so while your foot is off the clutch you can have the clutch pedal flush with the brake pedal like new cars.

If you have power brakes I've seen the master cylinder hung two different ways. One is to make a bracket so the MC is under the dash. The other is to have it in the engine bay, underneath the brake booster, at an angle with the rod facing up. The stock brake booster is too big to put the clutch master beside the brake booster. If you have manual brakes or a non stock booster this may be a non-issue.