Billy,
I don't have the typing skills/speed to truly explain all you are asking, but I can help a little. The two-stage clutch has 2 disks that are separated with a heavy plate in between, one disk drives a shaft for ground movement, the other engages a hollow outer shaft for the PTO. Part way down with the pedal disengages the PTO disk, further down disengages the drive disk. This sort of clutch is generally replaced as an assembly, and it must be set-up correctly on the flywheel or you will never get it right by adjusting the pedal.
If your failure was sudden and complete, you may have broken a clutch finger or some other odd sort of deal. But the original clutches in the older Branson/Century tractors would not take any abuse. A careful operator would get years of use, but a little too much slipping or riding the clutch would cause the disk to overheat and the clutch would fail quickly. They have since changed the clutch material. Gone is the super-smooth gentle engagement of the old clutch, however the upside is that the new clutches last really well and you can get used to the direct engagement. Many a times an early Branson owner would loan his tractor to an inexperienced neighbor and need a clutch the next week.
Unfortunatley, years ago we replaced a lot of Branson clutches (problem has been solved for years, so new buyers need not fret) and it is a chore on this model. Some tractors are easy, this one is hard. But if you just take it one step at a time, you will get it. It isn't real complicated, but they made sure that most every bolt is hard to reach so it is a lot of hand work and not much air-gun work.

Look over your PS hoses when you have it apart. If they need changed, now is the time.