Sounds like you definitely need a Service Manual
before you begin this task. I would recommend the one
in the list I have linked for your tractor named Gas and
Diesel Service Manual with 594 pages. I am going to
go against my normal rule of not mentioning this on
the forum but if you are okay with a downloadable PDF
version go to the Farm Manuals Fast site, it is legit.
That version is about half price. That engine is a bit
more complex with the integral deck plate and
cylinders. Whether it needs replaced depends on the
amount of wear in the cylinders so that is a wait and
see thing. YT does not look to have many parts for the
diesel version of your tractor. I am also not sure what
JD still has to offer for your machine. You can actually
look that up on line, see 2nd link. You will have to
select the nearest dealer to you to see availability and
prices. I hope you realize this endeavor will easily have
a cost of over $3000. I would also recommend you
place future post regarding this task in the John Deere
topic section.
YT JD manuals
JD 2010 online parts catalog