Hydraulic clutch pedal question

Putting the push rod down there on the pedal changes the pedal ratio. That's why the pedal has to hit the floor to move enough fluid.

First part is correct. Second is not. Moving the push rod closer to the pedal decreases the ratio (nominally 6:1) which moves more fluid from the master for a given movement of the pedal! It also increases the effort required due to the same reduction in leverage.

As YR mentioned, I had a similar problem with a homebrew setup in another thread in the 4-speed forum. I also moved the slave attachment point closer to the fork on the pivot (easier to do than removing the pedal and redrilling/welding the master attachment point).

I called Centerforce about it, asking about how much travel the throwout bearing needs, they said 1/2 inch.

That's a useful data point, although that probably includes the free play as well. Look at a fork and you'll see the ratio of the fork is around 2.5:1 (hole to pivot to throwout). That implies you need over an inch of travel at the fork hole, which I also found by experiment.

I lean towards keeping the master cylinder rod near the stock location not to affect the pedal ratio too much and moving the attachment point on the clutch fork to where you would get that amount of travel. Of course, you need to take into account the bore size of the master and slave cylinder. If they are the same, the travel will be the same on either side.

Good advice, since you don't want to over-stroke your master cylinder. Everything factors in to the overall ratio between the clutch disc and your foot. Pedal ratio, MC bore, slave bore, fork ratio and PP finger ratio. And you have to pick components so that the travel of both the master or slave is within ratings.
Where I went wrong is not knowing the effective piston diameter of my slave cylinder (a pull cylinder will have less than the bore size since the rod takes up part of that area). Anyhow, relocating the fork hole fixed it.