Try a larger pilot jet. Or at least a new one. Even if it appears to be "open" it may be crapped out. You can get new pilot jets from the catalog house of your choice. Im assuming its a Mikuni.
Make sure the choke plunger is not leaking.
In my un-scientific tinkering, raising the needle position has helped me up top, but not so much on the bottom.
Heres another thing...check
http://yzworks.tripod.com
A friend of mine, Glen, who is part of that site had alot of issues with his old 250 being rough down low after he rebuilt the whole thing, but he's got it running really well now. He might have some ideas.
Im also thinking reeds as someone else did. Sticky, or inflexable? That is once the RPMs get going theres enough vacuum to open them up enough? Leaky boot?
The worst case of being "pipey" I ever saw it was an old IT175. Man, when I was a kid we rode that thing for a month before we found out that if you just leave the gas on long enough, it actually got up and went! It was a complete turd for the lower 80% of the throttle. :uh:
Good Luck!