I too have this problem on my 00 KDX and untill the shroud MUST come off, its as Domino Dave said, one with the tank. On the other hand, I just sold a 92 YZ250 that had the same problem. I managed to "rip" the shroud off the one last bolt that was stripped in. With the shroud off you could clearly see the plastic around the nut which had been "rounded" instead of square shaped. I never got to try it but I was thinking about getting a color coordinating GI JOE and melting him and letting the liquid plastic fill in the "roundness" back to its original square shape. I read about this trick in the back of the old Dirt Rider magazine in their "Trail Tips" section, I'm not sure if anyone remembers those but it said to melt GI Joes to sort of "weld" plastic fenders back together, but I'm not sure if it will be strong enough to hold the nut while you try to get the bolt out. Btw, after you "rip" the shroud out, you will make the bolt hole a tad bit bigger, just be sure to use a washer with the new bolt.
Best of luck.....and if anyone trys it, let me know how it works!