A year ago, I never thought I'd be shooting 4x5, so at that time, the Canon 9000F II fit my needs just fine. Now, not so much. So I understand I have to make two passes for the 4x5, but I'm having a couple of problems.

First, it seems when I move the negative for the second scan, the software changes the exposure, which is really annoying. Is there a setting to eliminate any and all of the auto adjustments? In the manual, it says to set the adjustments to 'None', then hit apply, but even still I'm getting a variation. Photomerge seems to adjust the two images to emulate the same exposure values for each, but I'd still like to have them both scanned with the same values.

Next problem is when I stitch. I use Photoshop CS6's Photomerge, and it does a good job, but I'm getting a transition line between 'images' where the stitching occurs. I don't tape the negative to the platen glass, and was wondering if that could be part of the problem.

Before you look at the attached, there are a ton of things wrong with it that I'm aware of; A)The film was Kodak Super-XX that was in a film holder for an unknown number of years. B) I used box EV (ASA 200) when I used it (should have been around 80) C) light leaks are either from the holder or that the holder had not been properly handled over the years. D) Bottom of the image is essentially undeveloped (the FR tank uses a ton of developer, more then I realized) E) Just about anything else you notice

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This is a 90% crop just to show the transition line:

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