Long type clutches use the 3 pairs of bolts with the pairs being closely spaced. Most machine shops can use a machining index to mount the flywheel and rotate it in the mill with distance from center adjusted and degree setting of each bolt hole. All 9-inch inch Long clutches use the same distance and spacing so it's not a difficult job. Just bring them the flywheel and clutch cover for set up. Different diameter Long clutches have different distance and spacing to suit the diameter of the clutch.
Modern diaphragm and older Borg & Beck clutches all use 6 evenly spaced bolt holes and may have 3/8" bolts depending on the auto manufacturer's specifications.