Well I have an 06 and looking for a suspension. From what I have read the 06 and the 05 are different. The 05 has a smaller strut mount recession in the knuckle. The recession in the 06 is larger, so an 05 or earlier shock will not fit. If you want to use an 05 or earlier strut and spring kit, you need to change the knuckles. Once the knuckles are changed, you can use any lowering kit from earlier versions of the focus. And that should solve the problem.
Also note that I looked at a 05 next to an 06, and what was visible is that the 06 spring perch was flat, while the 05 had a raised edge around the spring perch. Not sure if I am using the right term, but it kind of looks like a sacure on the 06 and more of a bowl on the 05's.
As far as I know there are no struts for the 06's yet, rumor has it Eibach has them very very soon. As for the springs, I know steeda sells a set for the 06 for $250, and I keep hearing Eibach has a set, which I think you have.
But for now, we have to wait for new struts, or change to 05 knuckles, and use any of the exhisting kits out there. Good luck.
Let me know what you find.