The ".prc" extension is used in the Kindle for Android app for MOBI and KF8 (azw3) formats. The KFX Input plugin isn't going to have any effect on the handling of those files. (Some magazines can be delivered in KFX format, but those would have a ".kfx" extension.)
Most magazines use the MOBI periodical format, which includes images of the pages in JPEG format and also reflowing text for the articles along with links between the two, in a single file.
Converting the MOBI to EPUB in calibre will convert only the articles. You can use the Kindleunpack plugin to get both the articles and the page images, but then you would need to pick out the page images and assemble them into a separate file (such as a CBZ) yourself. You will lose the linkage between pages and articles.
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