Brian,
I know what you mean!
Go back to stock 122mm pull rods on the '03. Run the sag at 105 - 110mm. Don't go overboard on the shock rebound, and run as much compression as you can without things getting harsh. The '03s have a more relaxed rake and the lower rear just slows things down. If your using the pull rods to soften the initial action, have Les revalve it instead.
The '07 250 is a dramatic change from my '03. You just drive the bike with the front wheel and it goes there, period. Its the frame/subframe, the few less pounds, and the suspension. Also the 250s feel lighter than the 300s because there is less yank when the throttle is opened. Honestly, this bike is totally awesome. The perfect amount of low end power with just good jetting and an LTR PV cover. I have a difficult hill to climb, with a series of ledges 2 - 3'. You hit the first ledge on the left, and do an immediate 90 deg rocky turn across the trail (about car width) to hit the next at the right about 20' up. Difficult turn. Its easy on the '07, wheelie, turn, wheelie, done.