if you run a cv joint you have to point the pinion up at the Tcase(or really close, preferably 1-2 degrees below it so when your on the gas it points right at it) that means you have to cut off the perches and redo them like you said. if you run a standard Ujoint on both ends you have to match the angles at both flanges which may require tweeking the pinion angle as well.
the 2 standard Ujoints on a shaft cancel eachothers oscillations thats why you have to match the angle(and the oscillation)
on a cv jointed shaft you point the pinion up at the Tcase so theyres no angle on the Ujoint end, since the 2 Ujoints in the cv joint(double cardon) split the angle and cancel eachothers oscillations out....
hope that makes sense?
