If you know that you have particles in your reservoir you should remove them before even starting your build. In production manufacturers often use pickling fluid. I'm not sure what it is made of, but a good substitute is diesel fuel. This cuts any cutting fluid/grease/oil that can hold onto particles while at the same time keeping some anti-rust properties.
1. Insert magnet into reservoir
2. plug all the holes but one
3. add diesel fuel, slosh around vigorously
4. drain diesel
5. inspect, repeat if necessary
6. remove magnet, clean off particles, reinstall in reservoir near pump inlet
Another thing you could do initially is plumb the pump right into the filter and then to tank. This way any you can't contaminate the valve or cylinder.
I do like Hydtool's suggestion of a screen in the fill cap. This is cheap insurance. You wouldn't believe the amount of crap that can be in "new" oil. I once commissioned a new 200hp power unit using seven 55gal drums of premium Mobil oil. As I emptied each drum I looked at the bottom and was surprised by the amount and size of particles left behind. That is why we filled each machine using a filter cart, which is simply a cheap gear pump that sucks the oil out of the drums and passes it through some filters before dumping it in the reservoir.
ISZ