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ABBYY FineReader is currently considered the best OCR-ing software around. But it's not free, nor open. It does, however let you export to ePub, and in older versions at least in HTML format (which you can then import into Sigil). But ePub is not very good with complex layouts found in magazines... It's great for novels and such but anything above a single column is just asking for trouble.
PDF is better suited for complex layouts.
Unless you want to spend a lot of time proofreading the articles and go "vanilla" (no foreground image and background text), I suggest you apply the standard "good enough" OCR with FineReader and be done with it. It's still better than no text at all. Else you'll have to track down the fonts (or fonts that look similar), learn how to vectorize graphics, perform a lot of micro retouches and proofread the final product one last time. The quality will be amazing and it's always a pleasure to read something done right. But the time spent will be significant. You'll need to set aside a couple of hours each day to learn this stuff and in about a month, maybe two, the first magazine will be done. Sometimes it will seem like a chore, a repetitive, life sucking chore but you'll eventually start to get better at it and work faster. It's also very easy to get discouraged. Very few people stick to it.
Considered to be the best at layout and vectorizing: Adobe InDesign and Illustrator.
Open source and multi platform: Scribus and Inkscape
Have fun!
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