You need a cylinder liner pulling set. Shop manual recommends putting something over each crankshaft throw to protect it as you pull the liners. Of course you may already have the crankshaft out by that time, that's even better. There is usually quite a bit of debris in the bottom of the water jacket that will be dislodged as the liners are pulled.
Have you removed any bearings yet?
Usually can't fix what's wrong on one that did what you describe with an in-frame overhaul. Drop the pan and remove rod bearing caps to look. Then make further plans.
Yes.
Got a tractor here sitting outside the shop that is in about the same situation. Sounds as if the crankshaft has a bad bearing, maybe a main????, but won't know for sure without dropping the pan and the bearing caps.
Unfortuntately it will be parked in the weeds if the crank is the problem. A piston or sleeve problem, we might fix it.