Thanks very much to Matze, who sent in some feedback regarding the Media Center 2004 SP2 slipstream guide.
It would appear that the problem causing setup to prompt for files is the cab files used in the CMPNENTS folders no longer exist. By creating a 0Kb file called MEDIACTR.CAB in your \CMPNENTS\MEDIACTR\I386 folder and NETFX.CAB in your \CMPNENTS\NETFX\I386 it will allow installation to complete properly without stopping to prompt for mcdftreg.inf or SmartNav5.js. This is great news, especially so if you wanted to perform a true unattended setup. I’ve updated the guide steps to include this.