It turn over several revolutions. Probably about 2 minutes worth. Before we stopped it to check if we were getting fuel or not.

It appears we might be confused about the timeline and what actually occurred. Here is how I understand the events:
The tractor had set for three years or so and the main problem was the pony did not run.
You worked on the pony and got it to run.
Then you tried to start the tractor with the pony but did not give any fuel to the main, so after a couple of minutes you shut everything down. The pony was turning the main but was the compression lever left in the start or run position? When the pony was turning the main did the main kill the pony or was the pony “disconnected” and shut down like normal?
The pony still starts and runs properly but cannot engage the pinion and clutch to drive the main?
After trying to turn the main by hand you tried to pull start the tractor. Did the engine turn then or was it still frozen? Was the start / run lever in the run or start position?
Removed injectors etc and then would the main turn or was it still locked?
Are there two problems with one being the main still locked or is it now free? The other problem is the pony and pinion engagement. What are we trying to solve, the main being stuck or just the pony engagement and possibly a fuel problem dealing with the main?

That is correct the pony was the initial problem and I fixed it. I am not sure which position the compression lever was in. The main was puffing grayish black smoke out but would not fire ( because i didn't give it fuel). So I shut off the pony motor(normally) not realizing at the time that the main engine had to start to disengage the pinion on the pony.
The pony does still start and run I need to check on the compression lever. But with the injectors out I could not turn the main over by hand even when I tried to pull start it the main still wouldn't turn over.
The problems are the main being locked up and if the pony motor still being engaged or possibly damaged could that be causing the main to be locked up from the pinion engagement. The fuel issue was because I did not lift the throttle lever up out of the shut down position. Sorry I didn't explain it better previously.

I have a hard time believing that after the main turned over for that amount of time that it could be rust in a cylinder, I guess anything is possibly though. The old man I bought it from said he always pull started it because the pony had issues. It was a bad magneto. I should of had him give me a better education on the starting procedure. Lesson learned 😆

You are correct that if it turned over that many times it would not be a rusty cylinder that keeps it from turning. If it has a rusty cylinder it will usually turn a part of a turn and then it stops. If the main is "normal" you should be able to turn the main with the fan belt. You will need to push a hammer handle or something against the slack side of the belt to keep it from slipping on the pulleys but it should turn by grabbing a fan blade and turning it. . Make sure the compression is set to start before hand turning it. I'm assuming you have the injectors back in. Or like someone said the start run lever might be reversed.
Is the latch lever, the rear one, loose of does it resist when pulled up? When engaging the pony does it grind or just nothing happens? When you move the clutch lever does it have some resistance or possibly something is wrong in the clutch especially if the pony runs. Not sure but there should be a small access hole that you can remove to see the latch. Depends on the Model. That way you can see if the dogs are latched.
This video gives an idea of how the pinion and clutch work with the pony. Yours won't look exactly like this but the principle is the same.



Or search on Youtube for "d2 pinion" to get all sorts of videos

If this was my tractor with this problem, I would be removing the pinion drive from the flywheel housing. I get the feeling that something has happened and caused the bendix to become looked onto the flywheel. I can remember a lesson I learnt many years ago. A machine owner sold his loader at auction because a mechanic had diagnosed a seized engine. The person who purchased the loader gave me the job to remove and rebuild the engine, as I was removing the starter, I heard a slight clunk. It was the bendix retracting. I used a bar on the flywheel teeth and the engine started to roll. Tried another starter motor and the machine fired up. I believe that person ran that loader for another 10 years after that. In my 40+ years of being around equipment, I have came across stuck bendix drives two times, with the owners thinking they had seized engines.

Tractor dand2, I know that lesson you learned too 😆 early in my mechanic career we had a busy shop and I got sent to the field for a non start on a d11. They shut it down the night before and thought it just needed a jump start so I went out and it sounded like the starter was hitting hard when it engaged and I put a 3ft breaker bar on the crank and it wouldn't turned. I called the office and said it was a locked up engine. They sent another guy out he agreed so they sent an older mechanic out and said the same. We pulled that engine and the fly wheel bolts fell out and lodge under the ring gear. Everyone stood there in awe looking at it. I got a field service a few weeks later and a raise lol. Can you pull the pinion without pulling the whole pony motor?

D4jim,
I took the generator out and I used a 3ft pry bar on the gear teeth trying to turn it both directions. The latch lever doesn't seem like it moves anything no resistance at all now and there is no grinding when I move it. The clutch lever does have some resistance but I feel like it needs adjustment I think it should have a little more because it does not have a good "snap in" feeling a little light.
The injectors are back in. The machine is about 3 hours from my house so when I get back to it I will check the compression lever and make sure its in the start position. I appreciate all the help. I will open that acces and see if the pinion is released or not and see if I can trip the latch and release it. It could be stuck. I bought it at an auction and the owner said he was having pony issues so he always pulled started it. I just assumed the pony not firing was the pony issues now after talking to you guys I am wondering if it wasn't a pinion issue too.

The pony will need to be either removed or lifted up a few inches.
There is a transfer gear between the pinion drive and pony output that will need to be taken off in order for the pinion drive to be removed.

is the gearbox in neutral is the drive clutch engaged. the clutch should ALWAYS be engaged unless changing gears or stopping the machine as the clutch plates can warp leaving the clutch engaged prevents this from happening.

maybe some thing has broken in the driveline cuasing this problem or a foreign object is somewhere it shouldn't be.

can you slip the water pump on the fan belt ie turn it by hand even with the belt on they dont need to be that tight on these old things due to belt section size.
pull the rocker covers is something bent or broken.