Thanks for the tip, i'm familiar with the methods you mentioned, but i think what I'd need was something that added the extra polygons. The problem with the merge by distance thing is that it would not create new polygons, just move existing ones, and it would probably merge with it's neighbor polygons in many places. I was looking at meshlab because it has many things in it, including generating new meshes from existing ones, but i'm really not sure which option to use.Hi
You could highlight all the vertex for the object once they are lined up close enough, then choose Merge tool from the edit mesh menu, adjust the the threshold by clicking the square icon beside it and change as needed.
If they are real close or close enough, anything between 0.0100 to 0.0010 should do, use lower the closer they are to one another.
Judging by the screenshot, 0.0030 or lower should do you.
Unfortunately though, this will only sole the issue for vertex that align with one another.
You could try mesh-cleanup, to fix the extra edges left over not properly connected to anything.
Hope this helps