eveyone thank you for your replies !
First of all I am able to convert my epubs to PDF in Calibre and it displays the fonts fine, the problem is that I lose my chapters in the process, not sure why. I tried to add chapter detection based on <h2> tag but it's not working, I must be doing something wrong.
Peter Sorotokin: I created a small test file and your solution worked like a charm but again there are some major issues. First of all my books are in epub format and your tool accepts Word documents. Calibre can't export to doc so there is no easy way I can think of to automate this process, also if I just manually copy/paste the text in Word I again lose my chapters, plus of course all the book tags and metadata. But the embeded epub font does work on Nook so it definitely looks like solution would work if there was a way to apply it directly to an epub file.
I am still wondering if a rooted Nook can have its fonts replaced. I came across this
http://www.android-devs.com/?p=33 so I would think it's possible.