Wait a second. So what you are saying is that you are starting off with text (aozora bunko format?) and then you are going to convert into PDF?
In that situation, you should just convert it to a Kindle sized PDF, and then that will work fine on a Kindle or other 6" PDF reader.
http://a2k.aill.org/text.html <-- will allow you to convert Aozora Bunko formatted text to Kindle-sized PDF.
This will not allow you to use a dictionary though.