Unfortunately, I don't know much about Paint.Net and most of the regulars here either use Photoshop or GIMP. I know we do have at least a lurker or two who use Paint.Net as I remember seeing some maps, so perhaps they can pipe up with suggestions.
My first thought is that your color and B/W versions have heavily pixelated lines, especially around land/water transitions, while the original done in TerraJ does not. Not sure if this is something in Paint.Net or perhaps the method it was saved to an output format for posting here. Or perhaps you increased the size from the original image?
Next on your main continent, at the NW corner of the "cracked" earth part(desert?) and at the very Southern tip of the same, there is a really hard line, so you may want to look at blurring this transition to the grasslands a bit more. This is not horribly bad on the B/W version, but on the color version, it is really jarring.
Finally, you should look to see if any other techniques would produce more distinctive mountains. If Paint.Net has forums, you might also want to check over there to see if anyone has done some top down mountains and could give you some pointers. Also, check some of the tutorials here to see if any of the techniques used to make mountains might have a close analog in Paint.Net that you can emulate.
As for the text and labeling and stuff, you really do need some kind of scale to be able to determine what is too much if you get my drift. Also, you could always keep your main map without labels and drill down to create regional maps with more detail such as names for town, mountain range, , desert, forest,etc.
Good luck with the rest of the map.