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This baffle plate wasn't common on civilian 6.5's. It was used to prevent oil splash, reducing the potential of a leak between the IP and timing cover. Part # 14033820- Baffle, Crankcase.
Is the pump new or rebuilt?
Many of the rebuilt pumps have this problem because when they're rebuilt and run on the test bench they test fine at room temperature. Since a worn head and rotor usually shows symptoms when the pump is hot, the problem doesn't occur until the pump is installed and...
The hard start when hot problem is usually a warped head on the injection pumps head and rotor assembly. If it starts better when you run cold water on the pump or override the glow plugs this is likely the issue. Common problem with the 6.2 DB2 pumps.
You can make a paper gasket like that using a cereal box or something similar. Just trace the new gasket using the housing as a template. Skim a light coat of RTV on the new gasket and you're good to go.
All depends what year the 6.2 heads are. On the later 6.2 heads the injector angles are identical to the 6.5. I just put a set of '91 6.2 heads on a '97 6.5. No modifications were necessary because the injector angles were identical. That's why I said you "may" have to readjust the lines to fit...
I'd guess that's where your noise is coming from as well. A worn crank pulley or vibration damper will make it sound like a crank knock. And by your description, either one, or more likely both of those items are shot.
Just be careful removing the bolts from the small hole. If they fall in, you have to remove the timing cover or oil pan to retrieve them. I put a piece of blue shop towel or masking tape over the socket, then push it over the bolt to hold the socket to the bolt.
The 3 bolts can be removed through the oil fill tube. Just unbolt the tube and look in the hole and you'll see the topside of the gear. You'll have to rotate the engine to access the bolts.
No need to line up the marks before removal. Just don't turn the engine over after you remove the pump. I find it easier to leave the injector lines attached to the pump for removal and installation. It pulls off and on like a big spider with the lines attached.
Marine injectors won't add anything by themselves. It's the pump that meters the amount of fuel delivered, not the injectors. Both the marine and the stock nozzle have the same orifice size. On the marine version the pintle has more travel allowing it to flow more fuel 'if' more fuel is supplied...