Well. I did mine but I miss a spot...erasing is such a pain. too bad we cant just make a flood that transparented and floods the stuff needed for it.
I use GIMP (gnu image manipulator program) which is free, has a crap ui but has lots of features. I haven't used paint.net but people seem to get on with it fine so you could try that one too. Basically, there's free good image editors out there, don't use paint.
In GIMP you can use magic selection to pick all pixels in an area of similar colour based on a threshold you set, or you can pick an area of the same colour with another tool, you can use selection tools to isolate areas so you don't go over lines, I'm sure paint.net can do all this too.
I assume if this is using the alpha channel from the PNGs then we can do semi transparent textures too, btw.