Ok, so I've been flicking through some internet articles and here is what is confusing;
The charging system, as far as I am aware, is separate from the electronics in that it connects to the battery THEN the battery powers everything else - in theory. So, a fault with the charging system shouldn't cause a problem with the electronics on the bike UNTIL the battery is drained. If so, then why would the regulator cause a problem...
However, if this is to with load across the battery, then its ignorant to think that the charging system is entirely separate. It provides a Vdc across the terminals of 14.4 - so if it is faulty it will (in most cases) cause this value to drop but it shouldn't go lower than say the 12 Vdc of the battery itself (more like 12.6+ on a fully charged battery) until the battery is drained. This drop could be enough to cause the spark to become weak.
Now, as you crank open the throttle, you are pulling more air and fuel into the combustion chamber, right? So with more fuel saturation in the vapour, you need a stronger spark... if the spark is weak then you run the risk of a misfire... or stutter?
I assume this is what was happening?
Edit: Ooohh another thought - the stutter clears up at higher RPM right (at least for others) - could the increased heat from the larger combustions begin to counteract the weak spark a bit so that you avoid a misfire?