Sme more progress over the past couple of days. Yesterday I cleaned the transmission out and finished cleaning the steering clutch compartments:
   
I also shrunk the bearing cones out of the caps using a bead of weld, worked really well!
 

Today I pressed the new bearing cones onto the shaft and the cups into the covers and reassembled them back in with the shim packs exactly as they had come out of the tractor: 
The rotational preload on the bearings landed exactly where I hoped at just under 50 inch pounds (allowing 10-15 inch pounds for the pinion):
  
Backlash landed right at .25mm (.0098 inch) (unfortunately I never checked this when I took the tractor to bits but if the shim packs are exactly the same as what was pulled out I'm hoping this is close to what it was):
 
And this is the tooth contact pattern:
 
This is the first time I have ever set up a pinion and bevel gear and would appreciate anyones input and advice if this contact pattern looks OK? Toby could you advise?
 

I trust Toby won't mind, but I screenshotted a still from his video of when he was setting up the Bevel gear and pinion on 5J1113 (which has a 5U gearset):
 
Do you think mine looks similar?

 

Also, what torque should the bevel shaft bearing cap nuts be tightened to?

Both of those look like short toe contact to me.

I would be happy with that contact pattern, due to the drive pinion gear not being on an absolutely fixed axis because of the slight deflection caused by its ball bearing mounting, when load is applied to the gearset the contact will move upwards and land mid-range between toe and heel.  The contact pattern in the still shot from my video runs perfectly quiet under all loads, even when we drug the RD-6 around with it until its tongue was hanging out lol 

 

Sasquatch wrote:

I would be happy with that contact pattern, due to the drive pinion gear not being on an absolutely fixed axis because of the slight deflection caused by its ball bearing mounting, when load is applied to the gearset the contact will move upwards and land mid-range between toe and heel.  The contact pattern in the still shot from my video runs perfectly quiet under all loads, even when we drug the RD-6 around with it until its tongue was hanging out lol 

Thanks so much for the reassurance Toby, interesting that the factory setup of shims has fallen exactly where I want it with no adjustments! Even with the new bearings. BTW your picture of from your manual is much clearer than my reprint! I also had a question re the 1/2" UNF studs and nuts on the bearing caps, what would you suggest these to be torqued to?