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I'm sure I probably don't use it "according to manufacturers specifications" but I always use the dark grey stuff for everything. It would probably blend in with the diff. cover if you squeezed some out when torquing, too.
And I would not use any of any color on thet cover! Getcha a gasket and you won't have that mess to clean off next time. Any parts house will have a gasket for it. There are only 2 or 3 places on a complete rebuild that should have any sillycone on them.
Big Jim
OEM uses silicon sealant (Ford part # F7AZ-19554-EA) and it looks like Permatex black. I've used it on the rear end cover and it works just fine. For this job, use the Permatex instead of the gasket. When you do find a gasket you may be just as lucky as I was when you install it. I was tightening the bolts on the rear end cover and cracked it (it's plastic) at one of the bolt holes due to the gasket compressing.
Replaced mine on my 88' with a FelPro gasket and a thin film of Permetex black smeared on the gasket. Works great, but I have a steal cover not plastic. Not to much chance of cracking it, plus the tq is only like 15-30 if my brain is working this morning.