pull it apart, then compare your findings with what you see in the service manual's specifications. You're gonna need micrometers, inside and outside. Dial bore gauge. Torque wrenches. Whole bunch of other stuff. Dial depth gauge.
a lot of folks think just because it's a diesel, it's crude, loose fitting, throwed together. All 100% wrong. What you see on TV is false, it's usually edited, and always dramatized. Case in point, I was "in on" a TV show a number of years ago. THe show dealt with cars. They "bought" (were donated) a car to restore, and of course being "TV", dramatized--it had to be done in 5 days. What they didn't tell everyone sitting in front of the boob tube was that the restoration took almost 3 months, but they condensed it all down so that it looked like just a few days. And the viewers ate it up.
but no you just can't blindly go about it and expect it to work, and last.
Pull it apart in frame, then diagnose it using your tools I spoke of, compare your measurements to what the book specifies, and follow those specs.
If crankshaft or block is damaged, you're gonna have to pull the engine off of the tractor. Expect to have to do that.
I usually do a compression test. If any one of the cylinders is low, I'll check valve clearance and then do another compression test. STill low? Pull the engine and deal with it on an engine stand. L2900's are pretty easy to pull the engine off of.