on the exhaust side it really doesn't matter given the restrictions of the stock manifold design. If you were that concerned about cyl-cyl balance, then you need to contact Ron R or Dave@boostwerks and have them fab an equal length runner manifold. Besides, you have that giant restriction called a turbo in the flow path, so unless you are making big power (with an equally large turbine) you will not benefit enough power-wise to justify the cost of a header that can balance the exhaust pulse at the turbine.
The stock manifold is far from being balanced, but if you are running a CT, that small turbine is more of a restriction than the manifold (at the power levels the CT can support).