You have to find out if it is loosing spark or fuel. When it runs bad disconnect the plug wires one at a time and see if you can isolate which cylinders may not be firing and if there is spark there at the time.
Hello and Welcome to the forum family . Start the bike from cold . after say a minute of running, spray / sprinkle a bit of water on the header pipes ( touch with a finger if your so inclined ) to see if any of the pipes stay cooler or cold compared to the others . This would let you see which cylinder s are not running . If this test shows a cold cylinder then you must determine if its lacking spark or is it not getting fuel .
Have you checked the plugs , spark ? Replaced the fuel filter ? it may be starving for fuel if it runs well at start up then looses power . The gas cap may not be venting and this can also cause a starving for fuewl issue .
Go to Dynatek and find there warranty dept. Email or call and they will give you a RA number to return it. They test it. If it's less than a year they send you a new one, over a year they let you purchase one at a lesser (about half) price. Hopefully the new design is better. http://www.dynaonline.com/skins/warranty/