As I recall, the heads and phasers are really the only big change from Gen2 to Gen3. Turbos also. But mainly accommodations for the EGR.
This was from COBB-
Definitely a lot of changes. Compression ratio is higher than Gen2 as mentioned earlier, turbos are different (greater compressor efficiency at higher airmass per Ford's modeled CoE), HPFP runs a few hundred PSI higher at WOT, smaller port injectors, smaller direct injectors (although pressure increase from HPFP will actually increase total DI fueling capacity). Likely some other changes to cam profile and intake/exhaust manifold design as there are some VE changes in the factory fueling model. And an emissions category lower at ULEV50 (Federal Tier 3 Bin 50/California LEV-III ULEV50) which is really impressive - these emissions categories are determined by the total mass of specific pollutants (NMOG+NOx) per mile, not per gallon of gas used. So for a relatively high fuel consuming vehicle like the Raptor, hitting this low emissions category is surprising.
Who said coyote valve train and metal timing chain guides?