Stand-by...I'm taking some measurements and photos.
EDIT: Well...my photos suck. But I can tell you that I think I have 20 degrees between perch angle and pinion angle. The actual installed angles would be something like: "pinion= 12 degrees up, and perches= 8 degrees down". Neither of these sits level in the final position...but there is always 20 degrees between them. So if you want to put your axle on jackstands, and position it so the machined face of the yoke is perfectly perpendicular to the floor....that would set the pinion to "0" (true level). Then set your perches on the axle tube and set them to "0" (also true level). Then...simply rotate the perches 20 degrees forward and tack em in place. That will get you exactly what I have.
The problem with doing this is...every truck is different, and I'm not sure you WANT exactly what I have. You might not be happy with the stance of your truck...and you could totally end up changing the springs or shackles to make further adjustments. If you do...the perches will be several degrees off from where you want them (thats why I need 4-degree shims installed backwards). So this is why you should leave em loose and do the final tack with the driveshaft in place and the truck sitting on the tires. This is very easy to do, and as long as you have the u-bolts and spring plates all installed correctly and snugged up with the center-pins in the holes on the perches...its quite safe. Hook up the driveshaft, bolt on the wheels, and drop it down. The pinion should be pointing "nose-up" but slightly downward from the driveshaft angle by a couple degrees. If its not...just loosen the U-bolts and rotate the housing (using a jack under the yoke) up or down as needed. Don't over-think the pinion angle...its not rocket science. Regardless of where mine or anyone else's is sitting...your yoke needs to be pointing slightly downward from your driveshaft angle. Period.
As far as the other question about the center pin...I'm not sure I understand? I ended up scooting my axle rearward (moving the center pin of the springs to the forward hole on the perches). This was because the extra lift had shortened my wheelbase and I wanted to put my tires back in the center of the wheel openings. This also meant I had to pull my driveshaft out another 1" to compensate. You will probably have to do the same, and that's why the perches come with three holes on them.
Sorry if this sounds so complicated...its really not. Just throw it all under there and hook it up...it will look perfect until you sit the truck down. Then after the springs have wieight on them...everything moves around, and you'll immediately see what I'm talking about. It may take several "stance tests" to arrive at the sweet spot to get pinion angle, wheelbase, and stance all to your liking.