Is this flywheel or wheel hp?.
As for the down pipe size, what did the manufacturer claim.
I believe that the less restrictions there are after the turbine the better for fast spool up and power. The best you could do is to have a large down pipe with no silencer exiting just behind the front wheel

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I find it very hard to believe that a bigger down pipe and larger inter cooler would cost you power. More likely the chip is mapped for a standard engine, so it's not making the most of your mods. What was the hp with the mods before the chip?.
Steve.