I would assume that the pcm doesn't use the base open loop file while you are in PE so I don't see why it couldn't be set to stock?

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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)