So I don't align the powervalve with the hole (partly because my exhaust/valve have been ported so it probably isn't right anyway. You did right by aligning flush with the exhaust port. I'd just focus on that, take the exhaust off and align it with the exhaust port. Flick the ignition on and off a few times to make sure the cables don't realign.
If you want a quick way to diagnose your problem to get you a steer in the right direction then I'd do this.
Align the powervalve flush with the exhaust port
Disconnect the powervalve servo
Remove the carb air filter boot (eliminating the airbox)
Run the bike with no air filter
What this should do.
Remove the powervalve will stifle bottom end, but 6k+ should shoot off like a rocket.
Eliminating the airfilter removes any restrictions that might be present in the air intake tract. Whilst not ideal running without a filter, it will be fine for a short space of time. Unless a stone flicks into the inlet you'll be fine.
You should now be running the bike quite lean (so avoid prolonged wide open throttle). The bike should run better now than ever.
If it runs worse, it tells you your jetting is too rich. If it runs better then you know that you need more fuel. If it runs the same, then you know the problem lies elsewhere.
I am expecting it to be the latter, I'm expecting the problem to lie else where, but ruling these items out first, means we can then start to go more technical knowing that we've addressed the simple things first.