Yes, the pushrod is shoved back into the trans by the pressure plate, so with the trans removed from the engine, nothing will push the rod back into the trans.
The measurements on your rod look to be about right. There should be 0-4mm of pushrod sticking out of the end of the input shaft (as shown at 3:06 in the video) when the release arm is sitting at rest on the black plastic stopper, and there should be about 24mm of pushrod sticking out of the shaft when the release arm is lifted fully, as shown at 2:58.
Verify there is about 24mm, but it looks right to me.
That would leave the clutch parts themselves.
What was changed, just the pressure plate and the clutch disc? What about the flywheel?
When everything was assembled, and the clutch wouldn't disengage when the pedal was depressed, what did the pedal feel like, normal, or very light?
Do you happen to know where the release arm was when at rest (pedal not depressed) and then where the arm was when the pedal was depressed fully?
It should sit just below 9:00 or so at rest, and when the pedal is depressed it should pull the arm up to about 10:00, or just under the 27mm selector cover on the front of the trans.
When lifting the arm by hand, it should get solid at 9:00 and stop, as the parts come into contact with each other. Lifting it further will begin to collapse the pressure plate and disengage the clutch.
I have pics of the release arm and related parts here http://www.brokevw.com/releasearm.html



