At lower RPM's, the bike is mostly running off the battery, as the stator doesn't really start charging until about 1800+ RPM's.
The voltage from the yellow wires (checking each wire as positive and ground as negative) should be 50+ volts AC.
And .3-.5 ohms checking between each of the stator wires to the others (1-2, 2-3, 3-1)
As long as you are showing increased volts as the RPM's go up, it's probably not the stator. But it should be a little higher at the 4000 range.
Are you sure you have clean and tight connections at the battery?
AKA: Tim & 'The Adventure Cycle' VROC #24567, NEVROC, SteelCity VROC
"When life throws you curves,
Aim for the apex."