As i read this thread i wondered what kind of shape was the bottom end in just before the kit? Did you blow or seize a piston or did something else happen? Maybe it just has lots of miles on it?
When you double the power of an engine the force on the bearings is multiplied by four time. So, unless your bearings were in perfect shape before the kit you might be listening to bearing damage/slop that already existed before the kit but was unnoticable.
One way to check is to remove the head, bolt the cylinder back down..
Turn the piston around and just slightly beyond TDC. (At this point the crank/rod/piston are 'stretched out' )
Now hit the top of the piston with the heel of your hand. If you hear a "click" you are listening to excess bearing clearance somewhere in the bottom end..