In your admin/configuration/images can you post how you have your settings set up
am I understanding you right---you removed those folder/files you listed> they are there for a purpose so you should not remove them.
the image you upload should be the largest one that you want seen...for example if you want them to see a 900x900 image then upload that one size for each product and IH3 will take care of the rest of the sizes.
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