: Assigning the return value of new by reference is deprecated in /home/bingoman/public_html/wll_drupal/sites/all/modules/paging/pagination/pagination.module on line 508.
It's hard to tell for sure, as you included no example of your Zend_Navigation config, but it looks to me like your problem with the "strange URL patterns and presumptiions" is due to not specifying the route to use to build the link. this is very important to do when you have some pages using a named route, and others not, as when the url view helper is used to generate the link, if no route name is explicitly specified, it will use the current active route.
You should go through your Zend_Navigation config, and explicitly specify the route to use for each pages link, rather than use this workaround. When you don't want to use a named route you have added, and want the default route to be used, use the reserved name 'default' instead of omitting this parameter.
Fixing "The fucked up part"
It's hard to tell for sure, as you included no example of your Zend_Navigation config, but it looks to me like your problem with the "strange URL patterns and presumptiions" is due to not specifying the route to use to build the link. this is very important to do when you have some pages using a named route, and others not, as when the url view helper is used to generate the link, if no route name is explicitly specified, it will use the current active route.
You should go through your Zend_Navigation config, and explicitly specify the route to use for each pages link, rather than use this workaround. When you don't want to use a named route you have added, and want the default route to be used, use the reserved name 'default' instead of omitting this parameter.