Get em adjusted. Should be something to do every 25000 or 30000 miles. I know the sounds youre having too. Got a 01 myself with almost 45000 miles. I had them as well, got to a point where i started having to adjust my idle speed to keep the bike from dying at idle. Got mine adjusted, the intake valves were pretty off. No more sound, perfect idle and you get so much response and power back.
It's gonna be expensive. Shops know that a 2001 r1 is a pain to work on, so go for a shop that has a flat rate instead of per hour. It's a long job. it'll easily be around 300 or so, depending on where you go. Of course, a Yamaha dealer is much preferred.
It's worth it.