Alright, so thanks to the Frank Tzeng Gumroad tutorials, I now have adapted my style to be more hand-done rather than relying on alphas. I like my hand sculpted results much better than something procedurally generated (which I'd have to hand fix anyway.) anyway, this is what I have so far.
A lot of the details I'm finding will need to be tweaked after retopology, especially my hard surface assets. From hence forward I'll be more aware of these issues I'm having. The raptor body (4000 Tris) is a little high actually, but I want to see what I can get away with before I start hacking away polygons. Learning rigging has been very useful in learning topology. I'm also still a little unsure about allowing the raptor's leg plates to be geometry, but I think it should make the normal map look better. I'm not too concerned though, what I am concerned about is the amount of alpha going into it. So I think for a majority I'm going to have to come up with a way to fake it. Again, I also have to repair some high res detail in this too, especially in the hands. But soon, the raptor will have its Marmoset render and its Unreal Engine 4 render, and all will be well.