I have been running with Delkevic Marthy style exhaust, PC5, cut open airbox with all short stock Velocity Stacks for about 4,000 miles now. I believe with my set-up the airbox mods and short stacks enhance top end a bit. I bought a used airbox on E-bay super cheap, so I can play with Velocity Stack set-up. I was going to try all long stacks, but my bike runs so darn strong now, I do not want to change anything.
The only downside is fairly loud intake howl at WOT.