If it didn't vibrate before and it does after the longer shackle, chances are that it is a pinion angle problem. You can also check the angles with a magnetic angle finder with the drive shaft off.
the calculation is with the shackle 90 degrees to the frame, but it wouldn't change much if it...
The formula is: inverse sine (increase shackle length) / (spring length)
for your example and stock 42 inch springs it is: invsin (2/42) = 2.7 degrees.
This is an approximation that assumes that the shackle is 90 degrees, but it is good to less than a degree.
HTH