I just did a very similar project. I have a domestic hot water tank inboard. I replaced the shower hose with a garden hose so I could use hot water when rinsing the engine (it's very hot). I started with some Gunk and a variety of brushes. A stiff 2" paint brush is good for some areas, and toothbrush-sized nylon and brass brushes in other areas. After the gunk I hosed it down with the hot water and used full-strength citrus degreaser with the brushes again in some areas, then another hot water rinse. The citrus is good because it removes the oily residue from the gunk which would inhibit the primer from sticking.
I used plastic with hose clamps to protect the intakes and exhaust, but first stuffed a clean rag into each. When I pulled off the plastic the rags were damp.
But now it's all beautiful blue. For the topcoat I used Rustoleum Maui Blue. It's pretty close to the original Perkins color.
While you have the cooler out, I would recommend cleaning the inside of the plumbing. I found a ton of crud on both the fresh and raw water sides. You might check out my post on this, and how to get the brown slime out of the block: Perkins T6.354 Best Practice