I also have a 2000 R6 and I did what Heiko suggested -- drill the pinch bolt first then mark a point on the front of the fork to the right of the pinch bolt, 3 mm up from the bottom of the fork, then drill the diagonal hole at an angle that goes both to the right and through the bottom. You can drill the axle, but as Heiko explained because the nut on the left is lockwired (or should be!) you don't need to. Mine passed tech. with the pinch bolt and left nut lockwired to the bottom of the fork, but a better way is to drill the threaded part of the axle right through and use a castle nut and a cotter pin ... don't ask! LOL
P.S. Thanks to Jamie O'Grady (for noticing I was riding a track night with no nut and spacer!) and to Jon Watchuk (for the tip on the castle nut with cotter) ... way more secure!
Edit: "because the nut on the left is lockwired (or should be!) you don't need to" ... (there's no nut on the left, like you said) ... still, it passed technical inspection with just the pinch bolt lockwired to the fork leg.