This is a job I used to routinely do on my first Big Block Vette, whch had a solid lifter cam and therefore required close maintenance of the upper valvetrain, but is a job that I have never attempted on a diesel.
Does your manual give specific clear instructions as to the Yanmar recommended proceedure or no? Check hot or cold? Intakes before the exhaust or after? You need very clear unambiguous instructions first time thru.
If you have never done this job - even on a gas engine, the the smart bet would to pay a Yanmar-certified mechanic to do it the first time while you relentlessly peer over his shoulder during the operation.
Three-fourths of the Earth's surface is water, and one-fourth is land. So it is quite clear that the good Lord intended us to spend triple the amount of time fishing as taking care of the lawn.