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You might try looking at the HTML you created in a browser to see if you see a problem there.
You say that the HTML conversion created individual files. Were they all one to start with?
You may need to use a graphics program to break one giant image apart into reasonable sized images that can be displayed in an Kindle.
Calibre converts everything to an epub for display in the viewer if I understand it. It might display better in a program specifically designed to display mobis like Kindle for PC.
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