Wow, I have been out of touch! Looks really good!
I have a couple tips from my experience that may or may not help. To harvest your brine shrimps easily just use a straw, you know put your finger on it/cap it then put it in water and remove finger - suck up shrimps! I then put them in a shotglass with water from the tank in it to rinse them. Worked pretty good.
To protect them from the filter, you can get a little mesh bag from Petsmart to cover it with. They also have them with sponge type things, but I found it really restricted the water flow.
Sorry about your losses and I hope things are going well now!