Reading the map notes from Cobb for Stage 2 it requires a TBE setup, but I want to go a different route. Would running a Bosal Shorty DP and Bosal Catless UP, 2.5" Stromung Intermediate pipe mated to a Prodrive Oval axleback be a good enough setup to use the Stage 2 base map to its full potential?

You'll be fine, and basically using the map to its "full potential".