If you have the cage aligned so that it is parallel to the rings and the low limit screw set properly as you say you have then you may be expecting too much from your system. You should have some rub in the last two, or three gears. You can also shift up only one click of the shifter lever to "trim" the FD. Front Derailleur systems have relied on some sort of trimming to dial out noise. Hell, sometimes the chain rubs on the outer ring when you get down into those cross chaining gears. Now that is something you cant dial in.