They have moved the thermostat housing and changed some of the cooling hose configuration. I have seen with my own eyes an 05/06 Roush Charger installed on an 07 with these changes.
Software change as well. SCT has this figured out already though and has released the updates for programming.
Procharger has an 07 they purchased outright and they are just now beginning building their Tunes for the stage two kits with canned tunes. Their HO intercooled 2 core kit is already out.
Looking at the 06 and the 07 in the core / radiator support area, it looks like a fan change occurred (taking up more space side to side), and I believe intercooled chargers with larger diameter plumbing are going to have to make adjustments.