Yeah, I'd go with the WinAce front end. I've not seen his work in person other than fender flares, but he tends to have good reviews on here. I went with Greg's '11 Exige conversion, and it still takes a bit of fiddling (as is expected.
I think the headlights on the S3 really draw it out, so even if it could be made to work with the '06 headlights, half the progress would be lost. Of course just my $0.02. With the '11 Exige, it is less noticeable to keep the earlier headlights, so the project is far cheaper.
"Lots Of Trouble; Usually Serious"