Let's reason this out. You are saying that with the clutch pedal out, there is no engagement. Right? The slave cylinder extends to disengage the clutch. If the slave cylinder did not have enough throw, it would cause the clutch to not disengage and your rig would take off as it is started. Not the other way around.

The 3.2 clutch is a pull-type, not pull. This means the throwout bearing pulls on the clutch pressure plate diaphragm, instead of pushing on it. I know it has caused clutch install problems in the past. Most likely, you did not get the throwout bearing locked into the pressure plate. Sadly, whatever it is probably means that the tranny is going to have to be dropped, again.

Whatever you do, do not screw with the slave cylinder. It worked before and therefore, it should work again without crazy modifications.

Michael