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I am among the least mechanically minded folks here. You've taken off the airbox and opened up the exhaust, aren't these the kind of mods that increase top end power by sacrificing bottom end torque? No doubt a tune might might help but even in stock form these engines run better over 3500 rpm. You might consider changing the rear end with a performance gearing. I don't see how you can gain more low end with a tune other than fine tuning the available throttle response (how much available is the question).
I recall reading in a guzzi thread somewhere that the ecu from an 1100 sport installed in an EV greatly improved the response.