The intake flanges/pattern are slightly different, however if you use the '06 and up flanges on the '06 and up heads, they will fit on an '05 and earlier Twin Cam. Works the other way too. To use '05 and earlier heads on a later model you need to use the '05 and earlier intake flanges. The '06 and up flanges are interchangeable front to rear; the '05 and earlier are not. I assume that is why they made the change.