-I cannot comment on the 04 Ram blocks as I do not see Rams in any huge quantity. That said, I have seen hundreds of 04 Vipers over the years... even owned a couple of them. I have never seen any knock sensor bosses on any 04 engine blocks. Never, ever. Its not impossible the Ram may have been way-late 04 production or something and was wedged halfway between end of 04 Viper production, and the start of 05 Ram production... who knows. I have not however seen any evidence of this, and will keep my opinion until I actually see one of these blocks. It makes little sense to a manufacturer to do a "half-way" production, as it costs next to nothing for them to run the extra machine work and have fewer part numbers and changes.
-A custom PCM would be needed because the 04 truck with an 04 VIN should not be running on a 2005 PCM flash. The programming is inherently different, with potential differences in bus communications and routines. A dealer scan tool will incorrectly learn the year of the truck, and incorrectly apply updates. State inspections will incorrectly save vehicle year. Its a multitude of potential issues. The correct solution is flashing 05/06 hardware with a modified 2004 file to activate the hardware which it was previously lacking, and update the changes contained in the 05/06 tune, while still retaining the 2004 model year properties and label.