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I do not recomend the 3" from the catback toward the split because of back pressure and air resonance. I would do 2.75" with a x-pipe and then go 2.5" from the split all the way towards the muffler.
The pre-fabricated HKS Hi-Power for the GS400 are 60mm inlets. If you go with larger, you'll be creating a bottle neck (which may be ok because it'll keep some of the backpressure you'll be getting rid of with the large piping).