I'm trying to combine a 2003-vintage Ultegra Octalink 52-42-30 crank with an Ultegra triple front der (FD-6503 probably 2005-ish) with DA 3x9 shifters - all used stuff. Shifting works OK, but is noisy and rough, not nearly as smooth as my newer all-105 3x10 triple on another bike. I've gone through a couple tries of adjusting via the Sheldon Brown method and others, to no avail. Is there anything inherently incompatible with these compnoents?
If I'm reading your post correctly the only problem is that shifting in the front is noisy and rough. My suggestion is to try flushing out the shifters with WD40 followed by a few drops of lube. And if the shift cables or housings are more than 2 years old try replacing all of the shift cables AND housings.
It sounds as if you have the derailleurs adjusted but if there is any doubt try the instructions at Park Tool.