Can anyone recommend a good, free program for painting on a model that is already textured, but will modify the texture? I have searched online and there are so many different options my head is spinning. Thanks for any help.

Hi, snappertrx. The key word in your question would be "free". The first package that jumps to mind here is Blender. There is, obviously, a learning curve to Blender which many users feel can become quite steep. However, the texture painting tools there are nearly as good as any paid app, with some exceptions. The advantage Blender has over most other free 3d texture painting software is in it's stencil painting capability, which is very much like the advanced stencil painting tools in 3dCoat. This gives you some very flexible options to paint over seam borders, without worrying about texture smearing or stretching. It's not quite as robust and feature-rich as the stencil painting tools in 3dCoat, but it's still exceptionally useful. Most other 3d painting tools, like Sculptris, won't paint cleanly over border edges on a predefined texture map, and still many other free apps don't even offer a usable stencil painting option like this at all. Here's an example of the Stencil painting in Blender:

Stencil Texture Painting Multitextures

Sculptris is also another 3d painting option, with very simple to use painting tools, and great selection of alpha brush capabilities. There are a lot of limitations to Sculptris by comparison, however, and stability is sometimes an issue with certain models.

If the 3D app you use now can open the model and export it as OBJ, along with its textures, then you can use a free paint program like Krita to paint over the textures (if you know where to paint on them). Then re-import the model (or just the new textures if you already have the model loaded) into your app to update the model.