Sounds like a coil issue to me.
1 and 4 is a pair, 2 and 3 is the other pair.
Swap them over, like you suggested, and I am pretty sure the problem moves or even is solved.
Could also be pickup related but coils are more common.
I had the basic Hagons.. Hagon Road on my gsx1400..... i will never, ever recommend them to anyone.. even if they came free I will not fit them again.
They gave me very limited feedback and made the bike very unpredictable / wobbly in corners.
Basically it felt like i was driving with leaky shocks.
Apparently the Nitro version from Hagon is good.
Might i suggest these? http://www.jayguiracing.nl/ Harrie helped during the development of the "Rastec" exhaust. He has re-developed it for more performance and less noise.