setting up rear suspension

ok, i am fixing my rear setup because it wasn't done right the first time. it is a forward four link with the bags on the upper bars. as of now, i have the link bars in place. the lowers are parallel to the ground at half travel and the IC is towards the front of the truck.

first issue is the pinion angle. i don't think its right. the pinion angle needs to match the opposite of the transmission angle, right? but do i set it up at half travel or ride height, since ride height is much lower?

second issue is the distance from the axle to the transmission. i already had to move the axle back some because the drive shaft was pushing too far into the transmission when the truck was layed out. is there a way to find out a correct distance between the two, so that the drive shaft doesnt push in or pull out of the transmission?

The pinion angle should be set at ride height since thats where it will be driven. If your 4 link is set up properly, the angle shouldn't change enough throughout travel to be a concern.
As for the axle centerline, that should be set where it was from the factory. If its pushing your driveshaft into the trans, then I would shorten the driveshaft to work with the proper axle position. Don't sacrifice your wheelbase and risk having your wheels look offcenter in the wheel wells just to save a few bucks on the driveshaft.

so if i can find out what the distance from the axle to the trans is from the factory, then adjust my link bars in or out to match that distance, then it will be ok?

If you draw out your suspension and cycle it though the range of motion you can determine how far the driveshaft is going to push and pull out of the transmission.