Tannin,
It doesn't sound like you have a misfire condition; the compression is all right for that engine- not ideal, but all right. Since you say the shudder started after the clutch work, I would suspect a clutch, pressure plate or flywheel matter. Was the flywheel balanced with the resurfacing? Also, from your description, it sounds like you notice the vibration when the truck is standing still. Is that correct? If the vibration occurs when driving, does it change with engine speed or with vehicle speed? See if there is any change in the condition if you put the transmission in gear, set he parking brake, hold the clutch depressed and run the engine through the speed range where you would notice the vibration. If the vibration exists, I suspect you have a clutch/flywheel matter to deal with. If the vibration does not exist with that check, it sounds like a transmission matter- clutch shaft and bearing and/or the cluster gear and bearings.
Your acceleration matter sounds like the accelerator pump is not working properly. Possibilities there are the pump itself is leaking or the outlet check ball is not seating fully or the pump seal is leaking- the check ball would be the first suspect- sometimes the wrong ball is installed, or the ball is left out completely. Before dealing with the carburetor, make sure there are no vacuum leaks, and check/set the initial timing. You should also disconnect and plug the vacuum advance line, then see if the hesitation is gone. If so, you have a vacuum advance issue- probably the diaphragm is leaking, and the vacuum advance control needs to be replaced. You can check the vacuum advance chamber if you have a vacuum pump to apply vacuum to the chamber and see if it will hold vacuum. A quick check on the vacuum advance is to have the engine idling and quickly crack the throttle from idle to about one quarter (1000-1500 RPM) and back to idle. You should see the distributor rotate some (counter-clockwise) and go back to the idle position as the throttle opens and closes.
Hope this helps.
Harvester