Well the only thing that I can really recommend is looking at these tutorials; The Mapper's Tutorial and No1's Tutorial. Start using full raw instead of mixing autoborder. And yes, I mean even do mountains with raw.
So you will have a result such as this
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Instead of this
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You should also add onto your doodads so they only have these
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Instead of these
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If you need to know how to create a new palette look here.