I have used this plugin and I have to say it really is a bit bad programming so I had to resort to modify many parts of your code.
Ex. option pagination plugin modifies the default paging option that comes in wordpress which is really bad.
Always the categories are displayed regardless of whether or not products.
For every little thing the plugin always used get_option(), which increases in a huge way the number of queries to the database, I recommend you use the plugin "developer" and activate the "debug mode".
do not use get_option() to call the "Inner Template" instead uses do_action( 'wpc_inner_template' ) you better come.
Other than that I consider very good idea but will improve the code and logic I think it would be much better. Sorry to give such a low score Thanks.