Every thing I have read, said that the blocks were Aluminum for both 03' and 04' Mach's.
Being a limited production Car with 9652 built in 03', and 7137 built in 04', I don't see Ford switching over between model years, it is said that they lost $3000 on each one built, as it is.
The "R" in the vin is the engine code, designating the 4.6L DOHC motor (same code as the 69 428 Cobra Jet motor). The emissions difference is in the catalytic converters, 03' Cars have 4 brick Cats, 04' Cars have 6 brick Cats.
Cast Iron Blocks were used in Cobras, due to the need for higher strength (at a reasonable cost) for the stress of the supercharger. And on the GT, as a cost reduction measure. Earler N/A Cobras also had Aluminum blocks, the most desirable being the Tecskid blocks cast in Italy in the same foundry where blocks for Ferrari, and Maserata are also cast.