Sue
Very sorry to hear about your problems. There are a few workarounds to a few of your issues.
Using a dome port is actually a good thing. It overcomes the effects of refraction to bring back wide angle. However, using a dome port without proper spacing etc can make for bad images. Another manufacturer had issues with their dome ports with EX1 housings.
To work around the focus issue, I suggest you go into manual focus and prefocus to 1.5-3ft with the wide angle lens. With a 1/3" or small lens sensor, the DOF should take care of focus for everything behind it. That's for wide angle. You can also zoom in a tad until the vignetting is gone.
Red filters are miracle workers. It merely lowers the blue/green channels so that the red channel can look like it exists. However, to maximize its function, one has to manually white balance. Not sure if the housing allows that. Also it's most useful down to about 45ft, then light absorption makes it harder for the filter to work.
A possible workaround for that is to put WB in daylight mode. Then you can just color correct in post.
These steps aren't the easiest to use but at least you'll get some function out of your camera while you deal with Equinox.
Just realize that crap happens to the best of us. A reputable store recently told me they lost an item I sent for repair but forgot about, but when I asked about it, they said they thought they sent it back but have no shipping records to prove it. Perhaps I'm just too Cali boy but I just find the energy to get mad at them. That item is no long in production so they can't replace even if they wanted to. It's an object and the worse case scenario is you let your credit card handle this. They are pretty decent for disputes like this where they take the item and work with the manufacturer.
Good luck.