I have 4 photos.  Each of the 4 photos were actually stitched together with APP, using roughly 80 pictures each.  That part was easy since I used the Gigapan Import.
The shots were taken with a microscope, so it will be hard for me to retake the shot.  The effect I am going for is basically to create an abstract minimalist composition.

Each of the shots has tons of negative white space, but at the center are a lot of common points.  I try to manually move the pictures around and manually assign control points.  I am thinking I am doing a good job.  But then when I hit optimize, each of the 4 pictures jumps away from each other on the projection, and I get an RMS of over 100.  Something is way wrong.

1) How do I manually create the control points to link just these 4 pictures together?
2) Also I have vignetting.  How do I have APP choose good pixels over the dark vignetted areas, rather than blending?

Attached are the 4 images resized.  I've also included another file where I just manually moved them around in Photoshop, so you can see the arrangement. If you inspect the 4 pictures, you will see how easy it is to puzzle them together.
It is a 2X2 grid.

I don't do any normal panoramas.  But APP has been working for me so far. The good news is that it is just 4 pics!