I'm confused, how much did you underfill it? I can't imagine underfilling it a quart or two would ruin the motor. If it was a 14 quart system and you put in four quarts, I could see blowing the motor. How many did it hold and how many did you put in? Not trying to beat a dead horse, just trying to learn.
As far as engine swap, check with Kubota. I would think they could help. It could be a larger or smaller engine would bolt in. I know from working on cars, and I assume tractors are similar, that it is not just how the engine bolts in and mounts but how accesiories mount, how the engine mounts to the transmission, where the radiator hoses are etc. I don't know how much Kubota changed this kind of stuff over the years, so it could be you have a wide open choice of different year engines or it could be you are limited.