Welcome!!
It's common for Pony Motor Bearings to wear out (but it will never affect the magneto), new bearings are still available from Caterpillar. Your Cylinder with no compression could be due to a valve stuck open.
The smaller, horizontal lever coming out of the bell housing is the Starter Pinion Engagement Lever. The larger vertical lever is the Pinion Clutch/Brake Lever. The other lever as you suspected IS a compression release.
The Pony motor is geared to the Starter Pinion. To start the Diesel you first start the pony and idle it down. Open the Compression Release and then pull the clutch/brake lever to the rear to stop the pinion (and keep it from grinding) and then pull up on the pinion lever to engage the pinion with the diesel's flywheel ring gear. Once the pinion is engaged, push the pony idle knob in, rev up the pony and then push the clutch/brake lever forward to crank the diesel. When the oil pressure builds up you can close the compression release. After cranking the diesel for a minute or two you should be able to feel some heat on the diesel head, then you can open the throttle and the diesel should start to fire. Once the diesel fires the starter pinion will disengage (hopefully). If the diesel fires and quits, go back and engage the pinion as before and crank the diesel some more with the throttle closed. It may take several attempts with the pony motor to get the diesel engine started but you'll soon get the hang of it.
Good luck with your new toy!👍
Actually, it is possible for pony crankshaft issues to damage the mag. I remember seeing an old Caterpillar service bulletin that edb posted on here a year or so ago regarding that very problem. If either the pony flywheel is allowed to run loose on the crankshaft or the radial clearance of the crank journals in the bearings becomes excessive, it will build eratic vibrations in the geartrain that will transfer from the cam gear into the mag gear, usually resulting in missing mag gear teeth or a broken armature shaft. Since the mag is the weakest point in the system it usually suffers the damage.
I had this very thing happen on the first D2 I owned, my old 5J. I bought it from the previous owner with broken mag teeth and a dead pony, I replaced the mag gear and had it running good for about ten starts then it broke the mag gear again plus bent the armature shaft in the mag. I rebuilt the mag again and replaced the gear yet again, and this time found the pony flywheel was running loose on the crank, the tapered end was worn and the flywheel wouldn't stay tight. I replaced the pony motor with a good one and never had any problems again.
Make sure you have some backlash clearance for the Mag drive gear.