Update:
Still no solution, unfortunately.
The most recent attempt to fix the problem included several maneuvers: I pulled the air filter line off the carb and ran it briefly without the airbox and filters-no help. Next, I disconnected the vacuum advance line off the dissy-no help. Next, per the shop manual, I set the timing at 650-700 rpm to +2 to-2 degrees without the vacuum advance line connected to the diaphragm on the dissy-not much help. It seemed to run a little less ragged at 1200-1500 rpm, but not much. Finally, I gave up on the timing light and shop manual and played with the timing on the dissy at 1400-1500 rpm setting it by "ear"-not much help either. Ran about the same.
There is vacuum being pulled at the vacuum line, by the way.
With the new timing settings, I put an implement on the tractor (a soil conditioner) and attempted to drag our horse riding arenas (pure drag, no PTO used). The engine seemed to run a bit better at first, but the raggedness came back completely with time and seemed to get worse as the engine warmed up. No amount of choke or throttle adjustment seemed to help the problem. If I depress the clutch, the problem gets slightly better, but even then it persists, emphasizing that it has little to do with the load on the tractor or the PTO as I originally had thought.
To summarize the attempts to fix the problem may be of some value. The following have been performed:
1. Fuel tank drained and inspected (clean as a whistle).
2. New fuel tank stopcock placed with a fuel filter as the old one had fallen off.
3. Fuel filter on the old fuel pump was filled with debris and removed, the debris flushed out of the fuel lines and filter and gasket were replaced. Tractor was restarted and the this filter was reexamined and no more debris was found.
4. Fuel filter at the sediment bowl was removed, found to be clean, cleaned anyways and reinstalled. No debris in sediment bowl.
5. Fuel filter on the carb fuel intake line was removed (this is the fourth and final filter in the system), found to be clean, cleaned anyways and reinstalled.
6. Carburetor (original Holley) was removed, completely disassembled, soaked for hours in a gallon of carb cleaner, cleaned subsequently with compressed air and all passages were blown out with carb and choke cleaner. Then using an original CNH rebuild kit the carb was rebuilt to specs. The float had no leaks upon inspection. Carb reinstalled after all linkages were cleaned and lubed.
7. The governor was tested by opening the throttle by hand and revving the engine, it exerted a strong and proportional "pull back" suggesting it is working appropriately.
8. New plugs (gap 0.025).
9. Plug wires only 18 mos old. Inspected carefully for damage, none found.
10. New CNH points (set at 0.025), new condenser, new rotor. Dissy cap, an original Motorcraft part was also 18 mos. old and was inspected and found to be normal and reused.
11. Coil wire to dissy cap was replaced as old electrodes broke off upon removal.
12. New coil.
13. New fuel pump.
14. Allow carb to suck air without any filtration whatsoever-no help.
15. Multiple adjustments to the timing and vacuum advance as outlined above-no help.
The tractor starts and idles great after all of these changes, but wont run with power.
What have I missed?
Bad gas? The same fuel storage tank provides fuel to multiple other engines on the farm without problem. There is an appropriate amount of fuel stabilizer in the storage tank and has been since the fuel was purchased. The is a sediment filter on the storage tank which was last replaced 250 gallons ago. Fuel in the tank is approximately 14 months old.
Bad timing/bad distributor? I have learned that the timing advance is set at low RPM by the vacuum diaphragm, but at higher RPM by the centrifugal advance mechanism within the distributor itself. It seems that I have verified that the vacuum advance mechanism is not the culprit. The raggedness of the engine is clearly insignificant at idle and very reproducible at mid-range and high RPM. Does this suggest that I need to look at the centrifugal advance mechanism on the dissy, next?
I didn't think fixing this problem would be this hard.