A quick to get a cylinder/ring wear is to insert the rings in the cylinder and mic between the ring ends and compare with factory spec. 3000 hrs is not that much on a diesel unless there is a contributing factor creating excess wear. Many go much longer w/o an overhaul. Do you stop and start a lot. Just startup can add hours of wear.
As you did not mention your brand and model; why not post a question here on TBN to survey owners of the same tractor you have, on what their experience has been on wear/hours? That might help making a decision. If you continue I would sure mic everything first and compare with factory +/- specs. If in tolerance I would get new rings and a gasket set, de-glaze the cylinder walls, remove any detectable ridge, and put it back together and find the smoking problem elsewhere, its not there unless the rings don't seat right due to glazing.
If your engine is one noted for early wear; then I would be-build from the bottom up s other things are just down the road. Last thought; replace the missing fuel filter. The one ahead of the booster pump is the most critical. The one after, is double insurance or catch booster pump wear particles before the ruin your expensive injector pump.
Ron