It's so hard to predict future pricing. Maybe the tide changes and rare column shift cars become sought after? Who knows, if you want to drive it do what you wish, just keep all parts, cut sheetmetal, everything so as not to limit opportunities in the future.
IMO any deviation from an original Hemi though will affect value. Like today, if it was restored all else being equal, I could see it bringing 210K instead of 230K with a trans hack.