I just noticed my passenger side rear wheel was almost touching the rear of the fender.I realigned the rear and noticed the pad was missing between the rear and the leafs. My question is, what holds the rear from going forward or rear? when the perch is on the pin, the pin doesn't seem long enough to go through the pad into the hole?

The pin is located into the pad... and the pad locates into the perch.

The pad itself has a metal alignement dowel encased by the rubber of the pad. And no... its not really long enough.

I normally ditch the pads in all of my high to max effort builds.

on the rear leaf spring there is a "dowel"/nut that slipped into the shock plate that had a hole in the middle. I just did a hotchkis rebuild and I did not put the lower pad in at the recommendation of hotchkis. I believe this is how the rear end is aligned.

Even with the pin in the shock plate hole, you can still get a little (1/8 inch) movement front to back so make sure you measure both sides before tightening it all down.