You should double- and triple-check your stockpiles to make sure they're accepting the specific items you want. At times you will see logistical backlogs that may seem like your dwarves are just slacking off. Also, having a bone and shell stockpile that takes from your food stockpiles is entirely unnecessary, since bones and shells are never actually properly stockpiled there (though they may litter your food stockpiles if there's nowhere for them to be taken). Just make an indoor bone and shell stockpile and said items should get taken there eventually. Reason I said indoor is that bones, shells and skulls left outdoors will rot away, while you instead probably want to save them for ammo and decorations.
I don't know about work order processing while paused, but I really wouldn't worry about it. The rate at which an experienced manager processes orders - and gets more experienced accordingly - is insane either way, so you're hardly gaining an advantage because of that supposed bug.
A question of my own: is it possible for a dwarf to pass out from sunlight due to cave adaptation? I've seen dwarves - who had previously remained underground for years on end - sleep outside. Since they were neither soldiers instructed to sleep on the ground, nor hunters, it's weird that they wouldn't rather go inside to sleep in their grand or royal bedrooms and instead sleep in the grass while vomiting over themselves.