A couple of thoughts-- Unless a cylinder fired when you first turned it over the rod is probably not bent. I don't think a starter ever bends a connecting rod. If the rod were bent (and you say it runs but at about 75% power level) it would make a heck of a noise.
Do let us know the outcome.
Starters will bend rods, and quite easily. As mentioned if the piston is at or near BDC, and has oil in it (even a small amount on these tiny little engines), and the operator hits the key, the inertia of the crank, rods, pistons, flywheel, everything....will help "keep it rotating" in such a way that it'll easily, and almost effortlessly, bend rod(s). I have done it, on this exact same tractor, and another (M5040HD), both times I didn't even know it. The symptoms were low power, fuel smoke, and if you kill the fuel (remove wire from stop solenoid) and crank it, you'll hear one cylinder compressing less than the others, unless all 3 or 4 are bent, and if that's the case usually it will not run at all. No other noises, no knocking, nothing. Just a little smoke and low power. The 5040 even cleared the smoke up after it got hot. Had just enough compression to run, but only when hot.
Only time I've seen one make noise with a bent rod was on an RTV1100 that had one rod bent so severely that it was contacting the cylinder wall. And yes, it was quite noisy.
Keep in mind that Kubota uses a gear reduction starter, then the large gear reduction between the starter's gear and the flywheel. So there is a LOT of torque. Most engines built within the last 10-15 years are gear reduction starters. Gone are the days when direct driven starters were around, they were weak enough that if fluid was on top of the pistons normally it didn't generate enough torque to bend the connecting rod.
