the stop watch is very consistant. It's the operator that is causing the inaccuracy! not having a go or anything, but what's the best reaction time a drag racer can hope for? i think 0.4 seconds is a very good reaction time!
Anyway, some people use a video camera and film the squirt. They then replay the film in slow motion. Some cameras work by 'frames per second', and the duration can be worked out that way, but i doubt it needs to be that accurate.
Some bogging will still occur when smacking the throttle from idle, no matter how much you adjust, but did you adjust the pump timing screw? Small adjustments here can make a big difference. If it doesn't bog when riding, then i think it's the best you can hope for.