Wow- I am very surprised that you are able to turn the engine by hand. This is a good thing.
No offense, but- are you sure you don't mean that you turned the "belt pulley" (on the right side of the tractor). Since the belt pulley is hooked into the transmission, you will have to push the clutch lever forward to spin the engine.
Or did you turn the front pulley (just behind the radiator)? This would definitely mean that the engine is turning.
If the engine is indeed free, I would:
1.Fill the crankcase with fresh oil and remove the oil pressure sensor fitting from the engine block (follow the tiny tube from the oil pressure gauge down to the engine block)
2. Turn the engine a few revolutions by hand without the spark plugs, make sure there is are no scraping sounds and no "hard spots"
3. Look to see that the valves are opening and closing, if one is stuck open, spray some penetrating oil around the stem and lightly tap the top of the stem with a rubber mallet. If it just goes down a little further and stays, remove the rocker arm and carefully clamp some vice grips over the end and try to twist and pull it back up. My Case model S would occationally have a valve stick and it would bend that push rod. Don't worry, the push rods can be sstraightened.
4. Once the valves are working correctly, crank the engine with the starter and verify that oil is coming out of the block where the gauge tube was plugged in (this mean the oil pump is working). Then plug a good gauge in and crank it some more to get everything lubed up and see what kind of cranking oil pressure you have
5. Put a compressing tester in one spark plug hole at a time and crank the engine to see how much compression each cylinder has.
For the transmission, you can spin the belt pulley (the one on the right side of the tractor) when the transmission is in each gear to verify that all of teh gears work (jack up one or both rear wheels when you do this)