The off-the-shelf maps won't be specific towards having a map with a gutted up-pipe. If you want to utilize the best performance from it, I'd recommend ProTuning it (but it comes at a cost).
Either way, you'll be happy with the Cobb AP for bang for the buck for hp/tq gains.
Edit: Yes, you will use Stage 1 map. Stage 2 is only if you have a TBE.