two strokes rely much more on exhaust pressure to act as a "valve closure" of its exhaust port. it aids (and only aids) as a "wall" of air to cover the port at a certain instance in the stroke, to aid in compression as the piston reaches the top of its stroke. at some point, the piston will cover the hole for the exhaust port, and compression will commence. so it only aids, but its a bigger problem on a two stroke to have a proper exhaust.
on a four stroke, the valves act as the closure point, and the air is brought into the cylinder head directly, and the air is controlled mechanically (i understand i might be saying what everyone already knows) so the only effect that an unequal exhaust will have is the for the scavenging effect. with that being said, a harley davidson engine, and most of the engines we use for our builds, will not turn enough rpm to have this effect take place. especially in the case of a harley davidson engine (v twin, two rods on a common crank pin, will never turn enough rpm for this to matter)
so basically, having two unequal length exhausts is a very small problem, and can be corrected with proper fuel tuning, and will not have an effect worth worrying about on anything mild like our builds. on a high compression, high rpm drag bike? id worry a little more. cut away.......