For stitching images in the way you describe, we use the 'Photomerge' tool in Adobe Photoshop. According to the Photoshop tutorials, this algorithm works best when there is 25-30% overlap between adjacent images. So the images themselves are the fiduciary markers, and the algorithm figures out the final result by optimizing all overlaps available.
In our hands, this works very seamlessly 90% of the time and you cannot even see the edges of the original images. But no algorithm is perfect. Sometimes there are obvious registration errors, in which case we simply register the final images manually. Even if some manual adjustment is necessary, using this tool (or something similar) will save you much time.