I had exactly the same problem. What is causing this is the difference between a Diaphragm and Borg and Beck style pressure plate and associated throw out bearing.

If you're running a Borg and Beck you'll need a longer adjusting rod for proper clutch movement. Right now the bearing isn't contacting the pressure plate until the clutch pedal is near the floor simply because the pressure plate engagement rods aren't in the same location as a diaphragm pressure plate would be. Lengthening the adjusting rod will allow you to move the resting location of the bearing closer to the pressure plate levers so clutch disengagement will happen closer to the top of clutch pedal movement.

When I swapped to the Borg and Beck style I set up the clutch rods exactly how they were before the swap. I used pics I took before disassembly to verify everything was replaced exactly. After noticing the problem with the clutch pedal I removed the return spring on the throw out fork and I could move the fork rearward quite a bit before the bearing contacted the pressure plate and from that I could see the solution is a longer adjusting rod.