Sounds like quite a project! There are several ways to look at this. A lot depends on what you will be doing with the tractor.
If it is going to be a working tractor, concentrate on making everything right that makes it dependable, not so much cosmetics.
If it will be for occasional use, something you can show your family and friends what you did, then go more for cleaning everything up, stop the leaks, do a "best you can" rattle can paint job, go back with the right dash and aftermarket gauges, do whatever you want as for customizing the electrics. But be aware, this is going to get expensive, not counting your hours, you will spend much more that you can ever recoup from the investment.
If you are going for "show quality", this gets much more involved and expensive. Everything will need to come apart, down to the bare cases. It will need to go back with original parts, not aftermarket. That puts a whole new spin on the project, much more expensive and time consuming. As a novice, I would not recommend trying this as your first project.
The very first thing I would recommend would be buying a good shop manual. Spend some time with it, reading it through several times, familiarizing yourself with the project. Ask a lot of questions, do a lot of research, Youtube and Ebay will be your friends.
As for the engine, if it still runs well, I would leave it alone! Just clean it up, replace any leaking gaskets or seals, and set the lifters. Diesels are unforgiving beasts for taking any shortcuts or making assembly errors. Unless something just jumps out as needing attention, you will be money ahead to get all the life out of it you can.
To access the clutch, you will need to "split" the tractor. This means separating the engine from the transmission. Obviously you will be dealing with some dangerous and difficult to manage weights. Best to block up under the transmission, remove the front end, lift the engine with a rolling type hoist. This can be done by yourself, but going back together is easier with a assistant.
Try to manage this project as a series of small accomplishments. Looking at it as a whole will become overwhelming. Have a plan for sorting and storing parts as it comes apart. Take pictures, make notes, label the different groups. Ziplock bags are handy, storage totes for the larger stuff. Some large tables will be good for laying stuff out, but you will need a plan for storage, as the limited space will soon be overflowing.
Hope this helps, stay in touch, ask a lot of questions!
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