After looking at several videos (thanks to sheddcanyon) assembling the injection pump on my D6 5R looks fairly simple EXCEPT the part where you set the fuel rack. The gentleman showing the process has a special Caterpillar tool, a 3H1690 which is expensive to buy, even if you could find it. Is there another way to accurately gauge/measure the fuel setting on the injector pump? I do have the measurement of where the threaded stop was on the fuel rack shaft before removal but who knows if that was correct, everything else had been loosened or removed. Thanks everyone.

Not sure if that tool applies to a D4600. Looking at the service manual for the D4600, it calls for a 9B2532 Governor Setting Fixture and it describes an entirely different procedure than what. For what it's worth, I just returned the nut to its original position on the fuel rack, mainly because I know the tractor ran well prior to being parked. You should be able to get pretty close on high idle by adjusting full load speed adjusting socket located at the top of the governor.

If you don't have the service manual, you need to get it. Squatch's videos are a great resource, but not everything applies directly to this engine.

I did intend to return the nut back to the original setting if the fuel rack couldn't be accurately set. I'll adjust the governor setting as you described. I just called a guy today that has a complete, running D6 8U pony motor with electric start for sale only about 45 minutes away. I've read (on this website I think) that the only difference between the rope pull start pony on my 5R and the pony on the 8U is that it's just got the electric start but the bolt pattern, etc are exactly the same. My hope is I can swap it out with no adjustment necessary. Do you or anyone else know if this is true? I plan to measure the bolt pattern and take pics to verify.
Between the fuel injector, filter housing and governor off, hand clutch stuck, fuel tank needing cleaned, fluids changed, etc. It's not going to be running soon, but I'm pecking away at it little by little! Thanks for the reply and advice.

Same 3H1690 rack setting gauge used on the D4600 engine.
Pony motors are the same bolt pattern on the flywheel housing but differ in the water jacket head connections requiring a change in intake manifolds.

"Between the fuel injector, filter housing and governor off, hand clutch stuck, fuel tank needing cleaned, fluids changed, etc. It's not going to be running soon, but I'm pecking away at it little by little!"

Other than that, she's cherry!   

Old magnet: Could I take the intake manifold off of the 5R pony and install it on the electric start 8U pony? That would be nice if I could.

Yes, that will work.
You will also have to swap over the magneto and it's mounting cover as the 8/9U mag mounts at an angle for clearance and the 5R mounts vertical.

Good news! That's what I was hoping to hear. It's doable! Thanks Old Magnet.