This is where an older and wiser guy should jump in, because I'm not sure I necessarily did this right.
What you need to do is make sure the pinion shaft is parallel to the transmission output shaft, so that the angle across each U-joint is equal and opposite. As long as that's the case, you shouldn't have any added vibrations. The driveshaft angle doesn't really matter. (In this application at least. I assume for a custom build you'd be concerned about staying within some maximum U-joint angle, but you won't have that problem here.)
So the important question is how/where you measure each angle. I bought a magnetic angle gauge very similar to this one that measures angles from the vertical or horizontal. For the pinion angle, I put the magnetic base across the end of the yoke where the U-joint attaches. For the transmission output shaft, I used the face of the flange where my driveshaft bolts up, but mine is a '64 that originally came with a B&T joint, so your transmission might not have that. If it has a U-joint yoke directly on the shaft, you could do it the same way as the pinion angle. The only question here is whether the faces of the yokes are actually perfectly straight...
Once you have these two angles, adjust the height of the pinion with your floor jack until the two numbers are the same, or within a degree or so. I had the axle sitting in place on the new mounts, with the U-bolts installed loosely to the shock plates just to make sure everything was in the right position. If your engine is a huge torque monster, you'll want your pinion angle a bit lower to compensate for axle wind-up. Otherwise you might get vibration under acceleration.
Also, this might be a good time to replace your transmission mount. If it's old and shredded like mine was, it might affect your transmission angle.