OK, I'm just going to ask the simple stuff about your setup before taking this any further.
Please excuse me if I am just stating the obvious, but it is important that we all know that the basics have been carried out correctly.
When you first set the power valve positions did you:
a) Have a good fully charged battery in the bike. I stress this because I have had random troubles before that simply boiled down to a slightly crap battery. I think the NSR can be fairly temperamental when it comes to the state of charge of the battery.
b) Turn on the ignition (with the engine kill switch set to run) with the TPS and PV cables disconnected, to allow the PV electronics to set the pulley to what it thinks is the "Hi" position.
c) Without moving the power valve pulley, attach and adjust the cables so that both power valves are at the fully open position.
I am guessing that you didn't do this because something is wrong that prevents the PV electronics from rotating the PV pulley to the high position. Yes?
But the reason why I ask the a) b) and c) above is because I just want to make sure that you haven't set the powervalves to be fully open when the pulley is, say, in the fully closed position. This would give a situation where as you say: the problem is the power valves are always open when the bike is running. And the drive motor would be be fighting the mechanical movement limits of the power valves the whole time.
But if all the above is irrelevant (which I suspect it is) because you have set things up correctly, then it is time to try a new PV controller, or maybe check the signal coming from the pick-ups.
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[color=#808080][size=9]Yes,.. I too know how to waste Time and Money,...