The images are the first two scans made from images from a Compact Graflex 3 1/4 X 5 1/2

The camera came with a usable bag mag, so of course, I thought it would be fun to experience what photography was like a hundred years ago.

Film is a compromise. Aerial Recon Plus X cut to 3 1/4", so I lose 1/2 inch.

But the problem I'm seeing is this. The septums are wide enough to slide glass plates into. Thus my film sits .1" + or - back from where glass would be exposed. And so the focus plane I'm seeing on the ground glass is not where the image is landing. I don't know how to fix that. Any ideas. Cardboard inserts seem like a lot of trouble, but perhaps that's the way forward. Adjusting the ground glass surface to a different place seems beyond my skill sets. Daunting.

These were 1/1000 second f4.5 with a Cooke Series II 6" lens. A known sharp lens.

The film surface depth from the edge of the holder to the emulsion is .197 ± .007 inch for 2x3 through 4x5 formats so I can only assume the same standard was used for your camera and glass plates.
TriX and many other sheet films are .007 inch thick.

Its likely you have a Plate Magazine not a Film Magazine.
https://drive.google.com/file/d/0B1sPJkp-MdghNFVsYXk0a1dUTHM/view?usp=sharing
Film sheaths were made for plate holders.

With a ground glass at the film plane focus the lens on an infinity target at least 5000 feet away. Remove the view hood, loosen the view hood ground glass holder screws and reposition the view ground glass to match the film plane ground glass. Secure in place and reinstall the view hood.