I personally would suggest just starting with your stock bin file when tuning. That way you know what you got. If you start with an out of the box tune you don't know what has all been changed. Plus if you start from scratch you will learn so much more, and in doing so be able to fine tune your car that much better. just my

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Red 2dr 99 GTP: Z7 t66, A/A IC'd, Custom Heads, 65# Inj, ST2 Cam, Meziere Elec Pump, JP Double Roller(with machined crank gear), Plogs, PLX W/B, Powrtuner

99 Regal GS (work car)