Replaced my waterpump, thermostat, and fan clutch recently. Aisin recommends replacing the fan clutch and waterpump together, as they wear at the same rate. Seeing as the the fan clutch is coming off anyway to get the waterpump off you might as well for peace of mind. My waterpump had just...
Mines empty too. Manual says its an auxiliary box, has some straps in there too. Manual shows those straps as being able to hold down things inside so they dont move/rattle.
I always found bundling repairs and maintaince together makes sense. Just had my water pump, fan clutch, thermostat, and the belt with tensioner and all bearings replaced. Came to just over $600 in labour with the shop giving me a good rate for bundling. Preventive maintance is always the best...