Ok BeeJay42 - here is what I would recommend in your situation.
- turn off the tractor, remove key from ignition
- disconnect PTO from 
chipper, leave connected to tractor
- open up the chipping compartment so you can see the rotor, knives
  and shear bars
- check to see how sharp the knives are.  Does the shear bars have a
   nice, clean squared off edge.  The knives should be sharp enough
   to easily cut your finger.
- by hand, rotate the rotor.   Find which blade is closest to the shear
  bar and what is that gap between that blade and the shear bar.   My     
chipper recommends 1/32 of an inch.   If you have one - use a feeler
  gauge.  The remaining knives should not be that far off either.
- carefully spin the rotor.  Does it rotate freely.
- with one hand on opposite sides of the rotor - pull hard.  Go to the
  other side - same thing - pull hard.   You should not be able to move
  the rotor.  You are checking for runout.
- how big and thick are the chips.   They should be about 1/4 the size
  of a playing card and less than 1/8 inch thick.
Ok - this is the extent of my knowledge.  You have a hydraulic in-feed.  Is it adjustable.  I wonder - is it feeding too fast and not allowing the chipping action to function properly.   Why aren't the chips coming out the discharge chute.  Is there some type of screen that stops them from being blown out.
With your 90 hp tractor - it takes something major to stop the 
chipper and shear a pin.  Stop using the grade 8 bolts.  You will just continue to damage the PTO shaft.  Needless to say - stop using the 
chipper until you can identify and correct the problem.