There would seem to be a bit of conflict between your prior statement about pedal travel, and today's.
It is unlikely that the piston travel in the M/C is being used as the down stop for the pedal; typically the pedal will reach the floor before the piston bottoms.
If the M/C pushrod is indeed .5 inch short the clutch will not release. The eccentric, even when present, will not make up for that much clearance.

So you're saying that when the pedal is at the topmost position without being connected to the MC, the pin should line up with the clevis on the MC pushrod? Like I say, in my case the clevis is about 0.5'' off.

At the bottom travel end, it seems like the MC bottoms out about where the pedal hits the stop. I don't know if it's the piston reaching the end of it's stroke or something else on the MC stroke hitting something.

R:

Do you still have the old M/C? If so, compare the relationship of the mounting bolt bosses to the piston location of both cylinders. It is that relationship that led to there being two different pushrod lengths. If the bolt bosses of the new cylinder are higher (closer to the top of the cylinder) than on the old one, the pushrod will be "short". Similarly, if the piston snap ring is located farther down in the cylinder in the new one, then the piston will be "low", and the pushrod will seem "short".

Unfortunately, I don't have it anymore. I think I'll buy a new one to compare.

If everything was correct, would the back wheels be turning when I rotate the engine by hand with the transmission in first gear and clutch pedal pressed with the car on jackstands? All this time, this was my telltale sign to tell me if the clutch would disengage fully. But now I'm thinking, since there is absolutely no resistance on the drivetrain, maybe the wheels would turn since the slightest contact between pressure plate and clutch disc would make a bit of friction...

The investigation continues... I removed the transmission and clutch this weekend. Nothing seems wrong. The clutch was installed the right way and properly centered. All 6 pressure plate bolts were torqued to spec, although one of them was 5 mm longer than the 5 others. I cut it and reinstalled. I didn't remove the flywheel, but the shoulder onto which the flywheel centers on the crankshaft was flush with the face of the flywheel, indicating that the spacer used under the automatic flexplate was not installed.

On the gearbox itself, the clutch fork looks very good and not bent. Just by looking at it, you can guess that the force required to bend it would be very large... The pivot points were good, the throwout bearing is perfect and installed properly since it can only go in one way. The part where the slave cylinder pushrod contacts the fork is not worn.

On the hydraulics side, I received a new FTE master cylinder. It is the newer version made out of plastic. I compared the stroke with the old metal one and it's very close, but not exact. I took 3 measurements:
1- Stroke of the cylinder uninstalled
2- Stroke of the cylinder mounted on the pedal with pedal stop installed
3- Stroke of the cylinder mounted on the pedal without pedal stop.

Measurement 1 was 35 mm for the old and 37 mm for the new.
Measurement 2 was 28 mm for the old and 29 mm for the new.
Measurement 3 was 35 mm for the old and 36 mm for the new.

The conclusion is that you hit the pedal cluster at about the same time you hit max stroke in the cylinder. Also, removing the stopper gives you more travel, but when you install the pedals in the car you hit the floor before.

The bore of the MC and SC is 24 mm in both cases. So 1 mm of travel on the MC = 1 mm of travel on the slave.

The hardline is is good shape and not crushed.

While doing all of this, I remembered that I did not try the clutch with no stopper and no slave cylinder shim after I bled it with the oil can. Maybe it would've worked... I would have gotten more travel that way.

I installed the FTE cylinder and the pedals back in the car. I am now waiting for a new slave cylinder. The boot on the old one was ripped already. Maybe I'll observe a differend pushrod length...

I have pictures I'll post later.