Pony Motor Problems

it didnt make any strange noises when running?
it might have bent something.
pull the magneto look for damaged teeth/bent shaft.
check the oil level
pull the pilot heads look for busted pistons and what the water galleries are like

Your comment about the clutch would indicate to me to start there. Since you pull-started the tractor, we know it's not a pinion stuck engaged issue, so that limits it to the pony motor through pinion assembly. As trainz indicated above, removing the magneto and pulling the heads are very easy to do, so do that first. Of course for the heads, you'll need to drain the coolant but that's not normally difficult, and if the pistons can move, even a little, then they're "probably" ok, and you can refill the coolant. If the magneto turns over normally by hand, and the gear turns true/doesn't indicate a bent shaft, then you can set that aside as ok. If removing the mag does not free the pony up, then you can either refit it, or leave it off in case there is an issue with the timing/cam gear train.
But then that takes us to the pinion and clutch. Could you describe what exactly happens with the clutch? Does the lever "go too far" into engagement and beyond? If so, can you return the lever back to disengaged? Even if you can, you can pull the rear (well, front") cover off the pinion clutch assembly and take a look inside and study the mechanism while operating the clutch lever. If that's where the issue is, if you're lucky you might be able to poke around and move parts back into their correct place. If you can do that, then immediately adjust the clutch to confirm that it then operates normally, and that the pinion shaft can turn over ok. Also check for end float on the pinion shaft.
Then report back here so we can see where to go next. (which might be pulling out the pinion assembly)

Is the starter motor bendix on the pony motor stuck engaged? I have a tractor that sometimes bendix gets stuck engaged and it's easily disengaged by turning the flywheel backwards. It's easy to remove motor and check. Then try turning pony by hand.
Hopefully you didn't run the pony without oil. The crankshaft and connecting rods like to have oil.
Check the oil level in the diesel starter pinion clutch housing too.

Thanks everyone I haven’t had a chance to dive in I have been swamped working on the “bosses” she shed, and dad always told me happy wife happy life! Anyway i will let you guys no when I get a chance to Check some of these ideas.

Happy wife happy life, reminds me of the other saying, happy mistress happy Christmas.

Wombat

"No wife no strife!" lol

A little update I did have oil in the pony and i haven't gotten to look at the pinion yet. Hopefully this evening! However I did notice that it already has the hole for a direct starter just need remove the bolts. I have been doing a little reading around the website and it appears that it is a least a feasible option for hot starting. I would like to fix the pony motor though as I like to have that to warm the engine and get things moving before i fire off the main. Does anyone know what parts i would need? How hard it is to add glow plugs or some type of other type of pre heater? I've looked at the delco 50mt starters i believe? Although everywhere i turned on the site here it recommends the member "Old Magnet" and their website or information. I just seem to not have a lot of luck using the search feature.

Thanks again everyone.

https://sites.google.com/site/oldmagcat/home/getting-started

she who must be obeyed, the handbrake, finance minister, minister for war no matter what you call her when out of hearing range if she is happy or happyish life is much easier.
i swear mum has hearing like a bat. dad and i are just resigned to the fact were always in the shit it's just the depth that varies.

back to the real topic.
the minimum parts you would need set of rings, gasket set(never reuse old gaskets unless you really have too), carb kit(easy to do while you have it apart anyway), crank bushes & dowel pins, big end bearings, valve lapping paste, new governor belt, inline fuel filter(the cheap ryco one as found on many older cars with carbs), main seals