I'd suggest just hand painting out the issues you're having. Once you let go of the idea that a bake has to be "perfect" your workflow decreases big time. So the ears are kinda funky? just paint 127 127 255 (numeric value of color) flat blue over them to fix it. If you want you can take a black and white image of fur and…
So both the LP and HP are flat on these areas? If so I'd say your LPs vertex normals aren't all pointing in the same direction. This produces these gradients to counter the slightly round appearance of the LP.
dont remember how i came across this.. but one crazy idea that is pretty damned cool... http://66.70.170.53/Ryan/nrmphoto/nrmphoto.html and the main page with some more neat stuff.. http://www.zarria.net/