This is hugely complicated, but if you are interested in the keeping the driveline as staight as it was at full throttle then here's how to do it, assuming you know the maximum output torque from the gearbox, and that the old setup was OK.
I'm assuming you've got a live rear axle
1) measure the rotational stiffness of the rear axle system, in terms of degrees per ft lb of wheel torque. call this k
2) measure the installed angle of the pinion nose in the original installation, with the wheels on the ground. call this alpha.
3) Call the old axle ratio R
4) call the new axle ratio N
5) call the maximum output torque from the gearbox T
Then the new installed angle = alpha-NTk/R
where - means anticlockwise viewed from the left
In more general terms it is hugely complicated, and as usual it's a compromise. In an 'ideal' system using the centreline of the output shaft of the gearbox as the datum, then you set the diff centre on that datum, then point the pinion nose down a bit to allow for windup under torque.
If you can't put the diff on the datum then it is a good idea to point the diff at the gearbox output shaft, and then drop the pinion nose a bit.
Rule of thumb: UJ angles less than 2 degrees for good refinement (actually need to be within 0.3 degrees for some apps). UJ angles not to exceed 4 degrees at maximum torque. UJ angle at no load could be -2 degrees (ie pinion points below gearbox), so giving you 6 degrees of windup, if you need that much. Half of all the above figures is a better bet.
Make sure you understand the phasing of UJs.
Cheers
Greg Locock