I would not drill any holes in the overflow box. I've seen several keepers attempt this but they usually just end up making things more difficult.
Esox modified bottom skimmer is genius, but won't apply to your tank as from what I understand you have an enclosed bottom drilled overflow with a Herbie type drain setup.
If I'm reading you correctly, you're saying that the higher drain is the one youre controlling with a valve and the lower drain is completely open? This should be the other way around. Your lower drain is your full siphon and will need to be fine tuned with the valve, and the higher drain, right at about the waterline, is your emergency drain in the case of a clog. Here's a helpful picture to show you what I mean. If your setup is much different pls post a pic.
View attachment 1464405
As for the floating particles, I'm thinking you could probably eliminate 90% with reconfiguring your sump a bit and increasing your turnover rate. For instance, i would just convert the k1 chamber into a filter sock chamber. What is your flow turnover? What kind of pump are you using? Also, what size pipe are your drains?