So I'm a little confused by your 'mod' here. Since the instructions call for a polishing pad on top of the top tray below the blue sponge filter all you're really doing is plugging up the gaps around the outside? It sounds like you ran it w/o this polishing pad the first time and may be why you didn't get the smaller debris mechanical filtration you expected? The small little gaps around the outside shouldn't matter much if you have this in place as a small amount of water may get past this polishing pad but the majority of the water will pass through pulling out these floating debris you mentioned. Did I miss something or were you still having a problem with small debris in your water even with this polishing pad in place as the owner's manual describes?
All according to manual, with white pad. Try it "stock" and you'll see how significant the bypass is in what appears to you as "small little gaps".
I, too, am confused - about the fact that Eheim put such a faulty model on the market and that they even have success with it. Might be suitable for a guppy tank, I wouldn't know...
Small question, did you put the blue foam on all baskets or just the top one? also, i have a heavy stock in my 6x2x2 so i cant replace the top tray with floss only, but for the top white pad, did you get rid of the stock pad and replace that?