As a long time fountain pen user I can confirm that some of the Japanese nibs are
noisier than European or US nibs. This is normally classed as a feature and people move on. Any "scratchiness" however is probably due to a misalignment of the nib tines, simple enough to cure with care and a magnifying glass so you can see what you're doing - don't progress to using abrasives until you know what you are doing!
THIS is a useful guide from probably the best-known nibmaster >>>
http://www.richardspens.com/pdf/workshop_notes.pdf
For clean pen filling, even using removable piston fillers (aka "converters"), I would recommend getting a
plastic syringe and blunt hypodermic needles which make the process clean and enjoyable. At the same time, look on Amazon for a rubber ear-syringe - extremely useful for flushing out the pen and when you want to change ink colour.