I ran into a similar problem years ago, trying to place big block Ford toploader 4spd behind a 351C. I didn't want to swap input shafts so I took the trans to a machine shop and they measured the input shaft diameter (where it fits into the pilot bearing/bushing). They turned me a custom bushing from bronze, worked out good.
In your case I would either replace input shaft as mentioned or have a machine shop make you a custom pilot bushing from bronze (bring old pilot bearing or bushing so they can determine proper length). If you go the latter route, maybe grind the tip of that input shaft to even it out with the center section that's missing. Install with plenty of wheel bearing grease... good luck
