Have been reading Vizards yellow book lately and it seems as well as cold air and possible ramed air (although negilable) there is also inertia ramming or something similar which involved making the ram pipes / air intake longer in order to increase torque.
Anyway according to Vizard K&N brought out a torque master thing which looked very similar to what you have made. They stopped making them because they made it hard to set up the carburettor correctly. They were apparantly effective and it could be used to tame a lumpy cam and give you back some low down power without seriously effecting inlet flows at high revs.
It sounded a really cool idea, so just thinking you might be experiencing the 'setup problems'
The torque master strengthened air supply down low with a little cost in flow higher up so maybe the carb is running lean at the lower revs.
added to which you have cold air which means that you are getting more air into the cylinders which also means you will need richer jets.
also did you run it for a while and let it warm up because cold air I AFAIK can result in rough running until the engine gets to operating temperatures.
A whole lot of theorizing on my part but it may be helpful.
But it could be the way the air is flowing that is stuffing things up.