We recently moved to a property with 27 apple & 8 pear trees. They haven't been sprayed in years, and are mostly pretty buggy. We won't be eating them this year, but would like to save them for our cows/pigs. There is a brick storage building on the property that was supposedly previously used to store the fruit. there are 3 levels of wire mesh shelves. I imagine I need to line them somehow or the weight of the fruit will press into the wire. That's fine. But how to I keep the fruit flies out?  Also, it doesn't have a door, so we need to build one. Should it have some ventilation, or no? We are in the PNW, so it will be cold, but not super cold. Vancouver, WA area.

Apples are traditionally stored in cold storage so they remain in good condition, pick them before they are fully ripe.
On the racks you will need butcher paper (the non plastic filmed kind(it is brown not white)) lay a sheet of the paper on the rack and another sheet between every layer of apples.
Build a door that allows for ventilation, there also should be two vent pipes (like a good root cellar) for air exchange.
Install a thermometer or have one sitting on the highest shelf to monitor the inside temp. it should be around 45-55 f. for best long term storage.

The cold will keep the Drosophila melanogaster (common fruit fly) from doing any damage.

Redhawk

I've learnt a few things working on apple orchards about storing. Carrots will turn the fruit bitter. I don't remember exactly why but, pears were stored in a separate container from the apples, think it had something to do with one accelerating the ripening of the other.

One other key thing to consider is some varieties store better than others. The earliest varieties typically dont store past about a week or even a few days! So make sure you feed them to the pigs right away. If you can store them by variety it should help them store longer if you get rid of the ones going bad. You can also work out which are the best keepers for next year.

Apples, pears, peaches and plums are all affected by other fruits or vegetables both in flavor profile and ripening speed.
If you want bananas to ripen quickly you add a slice of apple, if you want peaches to ripen quickly you add a slice of apple or pear, this can be extrapolated along most fruits.

Apples that store well tend to have harder fruit.
Example; Arkansas Black is an apple that was developed for long term storage, the longer it has to sit, the better it develops that defining sweet taste.
They can be stored for up to a year.
There are many varieties that are considered and advertised as long term storage apples, usually these will also be termed as "cooking" apples.

Redhawk