First of all thank you very much for this updated version of WP Snap, which make things easier, especially its use with custom post types!
I tried to use your plugin in combination with some pagination plugins like wp-navi or simple navigation, to no avail.
I read here and there that some people tried to address this problem with the original version of Wp Snap (see http://wpquestions.com/question/show/id/1357), but using the proposed tweak code there's a glitch: the page parameter of these plugins appears before your own letter parameter in the resulting URLs.
As a result when you are, for an example, on page 2 of the A letter list: if you click on the B letter in the menu you navigate directly to page 2 of the B listing instead of the beginning (page 1) of the B listing.
Would you add to your plugin a way to handle pagination, or make it able to work with an already existing pagination plugin?
Thanks for your consideration!