You mentioned stripping out some of the markup. Does that mean you have Sigil? Or did you use some other tool? If you have Sigil, it should be pretty easy to edit the css styles to get your fonts bigger. If you don't have Sigil, I highly recommend it. I've found it much easier to get my files exactly the way I want them with it than by messing around with Calibre conversion settings. With a short period for learning curve, you can do all kinds of cool stuff to your files.
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