this is a tail end of a post of mine from hardcoresledder. Its easier to take off both your clutches and put the bolts back in and try to get them as inline or square as posible.
Then you loosen up your Pto bracket bolts and follow the rest (its from a eariler post I did from a coolant up grade on hardcoresledder).
I left my 3 bolts the hold the pto bracket to the frame alittle loose and then adjusted my center to center on my clutches, the adjustment for this is on the bottom side of your pto bracket plate, it looks like a little rubber stopper. The measurement your looking for is 12.2 inches or 12 1/6 inches.
After you get that set make sure you remeasure after the Pto plate is tightened. Then reinstall clutches and get your clutch alignment. Torque the clutches down to specs (55lbs on the primary).
After its all done, give a once over make sure you didn't forget anything, and run the sled for a bit and then come back check the Center to center and re-torque your primary and you should be set!!!
Well hope this helps if anyone has something to add go ahead. Some of the no-brainers I left out.