Enduro Nut, I too have a .46 in my 2001 503 V-cross. The forks are shorter on my 2001 than your 2000. By almost an inch. I have my forks up one ring on my 2001. On the 2000's I slide the forks up as high as I could to get it to turn as well as the 2001. I also cranked the rebound to 3 clicks out to help hold the fork down in the stroke on the 2000 I had here. It helped. I think the stiffer spring, sliding the fork up a bit, and messing with the rebound will make you happier. I also found Yamaha "01" fork oil to be too light for my 2001 and went to "02" and found things better along with the stiffer spring. But I'm a load.
Family, I haven't had any parts issues with the 2000, 2001, and 2002 models, despite what you might hear. Brad is VERY proactive with his folks. Over at Thumper Talk> Exotic Bikes there are a bunch of VOR customers chatting about their real time experiences should you want to hear from someone else. Brad also happens to be a VOR tech center and can really help should issues arise. Especially since you are within driving distance. Another Brad Benifit is he knows the trails systems along the front range better than anyone. Period. He's also a RMEC officer/ref and is at ALL those events with support. He also is very active in Ice racing to keep things interested during the winter. Look at all the trophies in his shop sometime...they are all his. He's an ex-IBM'er who decided to make Motorcycles his life. That 450 demo he has had since April last year was the bike he got "rider of the year" at the Colorado 500 last summer. No one works harder than that guy. Not trying to gush, just I have seen Brad in action over the years.