IOS – n iPhone App for reading PDF files

My solution was to use simpletext.ws, since the source is available I can use my own server to sync notes in my local network without having to worry about encryption. And on the iPhone I use the WriteRoom app to search and edit notes.

(As this is my first time using any stackexchange site I'm not sure if I should include this in the original question or answer it myself... apologies in case I'm not following the proper way of using the site.)

PDF files are popular precisely because the formatting is fixed. A PDF author can be sure that their document looks the same on any device that displays it. So I'm afraid you're asking for a feature that goes against one of the basic premises of the format.

That said, some PDFs have a text-only layer that can be displayed directly. On an iPhone, I'd recommend Goodreader for this. It will display the formatted PDF, then you can click to display the text-only version. That version may be bigger and more legible for you.

Having a text layer depends on the author of the PDF, but I would think Goodreader may be a step in the right direction for you.