Only the Roush Phase 1 has a powertrain warranty. And only on the original 3/36. Wasn't applicable for the Phase 2 kit on my 2011.
They offer one for the Phase 2 kit now: http://www.roushperformance.com/pdf/...de_10-1-14.pdf
There's one for the Phase 3 as well. Price goes up of course.