You seem well aware of the relative merits of the devices. Here are a few more out of the box differences:
Kindle advantages: keyboard, 3G model available, 4G internal memory, Text-To-Speech, MP3 support.
Nook Touch advantages: touch screen, less page-turn flashing, EPUB support, SD memory expansion port.
I sense that you'll enjoy the rooting advantages of the Nook Touch.
I only caution you that PDF is non-ideal for either ereader. Be aware of the limitations of both devices' PDF support and small screen size for viewing PDF. Without reflow, the resulting need for horizontal scrolling can make for a miserable reading experience.
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