Congrats on the new project. You can get any parts you need for the engine here

http://www.herculesparts.com/index.html

Since you say it is running what I'd like to do is run it for awhile and find and fix any oil leaks change the rear-end oil and the hyd. oil make sure the brakes are good or repair if needed. Then once you are satisfied I would start the restoration, tear down cleaning and painting, engine overhaul, any good local Diesel repair shop would be able to repair the injector pump and injectors.

I would also suggest joining the International Cockshutt Club, they have a quarterly magazine that is a great help to any collector.

Best of Luck

Joe