One thing that doesn't look quite right after baking everything are my seams. They look welded in the baked version, where the calculated shader version looks more like the hand painted grungy beaten up corners.
If it'd be handy to look at the model I can probably get that uploaded.
Perhaps it is the resolution on your texture? But yes, post images of the problems when you can. Also, remember Blender is tricky when it comes to exporting a texture and importing it back, there's a specific workflow. JL talks about it here:
https://cgcookie.mavenseed.com/lessons/color-managing-textures
I know what you mean - once you bake it you lose the ability to use box/tri-planar mapping and so the seams are more obvious. Unfortunately, there's no automatic way to solve this, but you can use the clone stamp tool in texture paint mode to fix it up. An example of that can be seen in this video about 13 minutes in: https://cgcookie.com/lessons/projection-painting-the-longboard
Thank you Jonathan and Omar.
I've been messing with the home network and haven't had a chance to post my work. IPTables and getting the port forwarding I want done is being a bit more stubborn than I'd like.