I'm gonna look into it again in the near future. I already have the GT350 manifold but running the stock throttle body for now.
My understanding is that SCT either doesn't have the data for the GT350 throttle body or does and won't release it to just anyone. Without that information, its very time consuming to get it dialed in correctly. This is based off what my tuner told me here in AZ. Not sure about HP tuners though....
As far as gains, I've heard little to none... But hopefully I'll find out for sure in the next couple months.
Send your stock throttle body to www.maxbore.com and get it opened up to 85mm for $100. Near the same size as the GT350 (with a couple better features like knife edging the blade, cutting down shaft screws) without the tuning headaches.
Or find a used 85mm. It's overpriced as hell but it's zero hassle.
I can see the advantage for s550 guys running the 350 manifold, TB, and intake together. For us 11-14 it's a ton of hassle to run 350 parts and the differences aren't worthwhile. CJ setups make more power anyway.