Great write up! Regarding the valve clearances...as I noted earlier, on the WR250f's the factory clearances are very tight when new, right at minimum. If the street bikes are that way too, as another poster noted, then it is likely the WRR's are set up tight also. Why tight? Valve opening duration is maximized. Larger clearances might also increase wear rates -
About the abrupt throttle....mine is smooth and progressive, stock. It is no more grabby than any other bike I've owned. My bike has no flat spots anywhere either. The only mod to the bike I've done is the air box flap removal. I wonder if the throttle issue is a production run thing?