They are not great on returning emails. they have good customer service if you call them. They were a respected tuner here in texas but then they moved to Utah, you dont have to worry about not getting you ecu back from what I have heard the turn around has been pretty fast.
Cobb is a large tuner they are just less talked about because most of their tunning is done in house they dont like to just sell parts they like to install and tune it safely.
They sell 2 versions of the ecu reflash one is just a reflash. the second which is about 100 more comes with a module that they can load different reflashes onto or email you the maps and you can reflash the ecu yourself. It does NOT allow you to tune the map it only allows you to load a premade map. So if you upgrade some parts and cobb has a off the shelf reflash listed for those parts they can email it to you and you can flash the ecu yourself free of charge.
now back to the turbo backs, as long as a ehaust is of the same diameter it will flow about the same amount of air so the tunning will not be much different. The only way the tune would be any different is if you got it dyno tuned but since you are just gettin a off the shelf map you wont notice and difference in performance between turbo backs sicne the off the shelf reflashes are tuned to be very safe.
No, you do not have to pay $400 again - I think they charge $20 - $30... I don't remember exactly. Soon they will be coming out with the AccessPort which will allow you to do the reflash for free at home. Check out their website for details. Any turboback will work for a Stage 2 as long as fulfills the requirement of a turboback. Their website also has their contact numbers, so I would just give them a call.