Watch your output settings with pdf exporting. Double check that your resolution won't get downsampled to much.

The way you've created your file is quite tedious and precise (think of the use of paragraph/character styles). Look for some step by step tutorial on the web -there are really hundreds of them. They've really helped me out.

Last thing I could come up with is finding the beginning of every line with GREP and insert a em-dash or something?

If you only got 1 line sentences you could you the paragraph rules (below or above). 

Mostly EPS files are way bigger in file size then Illustrator files. I wouldn't convert just because. 

I've only dived once in the Epub format and I faced the same problem; Abobe just published a nice article on how to handle the Epub format. For now I know you have use paragraph/character styles consistent. 

Yeah, the forum is acting weird lately. Stretched out pagenumbers and such. 

Have you created/applied a table/cell style? Things like the width should be controllable within this style.