Since the pinion yoke on a ford 9" is offset, how should the axle be centered? I'm going to install the driveshaft soon, and I need to know how to center the axle before I weld the perches and tighten the u bolts. Can the driveshaft be at a horizontal angle for normal driving conditions and offroading? This might be a dumb question for some of you, but i'm just not sure and can't find information about the subject. This is also necessary because i'll be adjusting my front axle to have an ideal ackerman angle.

measure from the backing plates in

Center the axle just like normal. If you don't center the axle, well, the rest is obvious. One side is going to stick out farther than the other.
Yes, there is an offset, but as long as your pinion angle is is the same as your rear output angle from your transfer case, you will be fine. The main thing is to ensure that your axle is installed straight in the truck and square in relationship to your frame rails.

thanks. that is all the information i needed.