Another cheap & simple option is rubber banding small aquarium media/filter sacks around the inside lip of the inlet bulkheads in each container. Problem is.. besides having a sack floating around next to the roots.. is you can't really filter out the last containers in the line/rows unless you got big 2" or bigger pipes or return manifold that the bags can suck into a ways without getting constricted and clogging up. Well..
Some early systems I designed awhile back would use a sacrificial container (same height as the rest of the containers at least) without a plant at the end of the row/s, and then run the return line to the pump from that bucket. Just hang one giant filter sock inside it off the bulkhead to catch any and all debri without ever clogging. Best RDWC system filter money can't buy on the market for some reason, but can be made for cheap if you don't mind the extra sized container taking up a little more space.
Otherwise, I would say your better off installing another extra inline y-filter right along side the original. If you added a T or better yet a better flowing Y fitting and had 2 of the filters, both with their own inlet and outlet valves leading back into one line again, it would allow you to run both filters at the same time by opening all the valves if you want. Or you could even switch one filter off, and swap between them every week or whatever, or clean one out without stopping the whole system by leaving the other opened up, etc.
Might just be cheaper and more practical though to buy a big 2" y-strainer (with reducer fittings on each side to match the current plumbing) with a way bigger pickup screen tube for $50-60 that has double or triple the surface area to prevent clogs. I prefer the chonky Banjo 2" y-strainers. You would think alien would go ahead and provide a decent sized filter like that now days, made way cheaper for low pressure hydroponic systems like ours... ah well.
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