So I finally got the sump running. Still tweaking and learning. Any tips or suggestions greatly appreciated!
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You can get creative and create a "screen" where the water drains out of your refugium so that it catches any small pieces of chaeto prior to entering your return chamber. Joann Fabrics or other fabric stores have a backing used for crocheting (I think) that you can get in 1/8 or 1/4 inch square holes that works really well.
To piggyback off this, you could go with a sponge that will fit snugly into that chamber and catch debris before it goes through to the return pump area. If the idea is to just stop the chaeto from getting in, maybe even eggcrate would help just create that catch for you.
A lot of people use a 100% polyester floss that they change out regularly in between the baffles as well. You do have a couple options that could work for you. I know some people just buy bulk off Amazon that is non branded toward fish tanks, but I haven't tried it personally.
Something like this below -
https://amz.run/44SU
I do like the water sensor approach in case of clogging overflow. How many holes do you have in that PVC drain pipe? I'd be weary of them getting clogged over time, might want to include cleaning that out on the regular maintenance list.
In terms of polishing the water a bit more, how old is the tank? That could be a sign of a bacterial bloom if it is fairly new. It could also be microbubbles from the skimmer going crazy or being broken in(which I doubt though).
That being said, try waiting a bit to see if it clears up after things settle down a bit. If not, there are options on that front as well.