I already went through that crap... I thought I finally had it.
I reshaded the whole thing three times now, then threw the old texture over top and then changed the lighting accordingly, though it is messy as hell I'll admit.

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I'm not going to lie I've come quite fond of how the bark is looking.
Wanted the whole flow of the tree to run from the top to the bottom, dunno if that was achieved or not.
Anyways I did the new update before reading your comment hopefully it clears anything up..
I'm really just cleaning it up as I go now, though I still need to get started on the leaves.