The stock setting will run a stock map, so it would be like running without the UTEC. If you run the Stage 2 map until you get a chance to get a tune you should be fine.
Now the BOV-H will probally give you some problems. You should get a recirculating BOV. With a stage 2 setup that BOV s going to lose you more power then anything else. The reason is your ECU expects the air venting out the BOV to be plumbed back into the system not released into the air. So your ECU will think its missing air and run rich and stuff. Search there are a ton of BOV posts to explain this. Just use the stock BOV or get a recirculating valve, otherwise run that one until you get sick of losing power then go back to stock or something better.