I've got a S Works E5 road bike and it currently has an integrated FSA headset which has a kind of carbon cone which is about 2 cm between the head tube and stem-it is part of the headset and not simply a spacer. Can I use another type of integrated or semi integrated headset like thisas I am keen to lower the bars a bit more. cheers..

The 'cone' on my S-Works E5 is removable, its not part of the headset. I have removed it on all my E5's over the years.

ok , i rather fancy one like the one in the link, would that fit ok?

I have no idea sorry.
I do know that a number of the early E5 Sworks frames were sold cheaply by CRC about 4-5 years ago (maybe more??). They were grey import and didn't come with a headset and there were lots of threads on various forums asking for information on which headset to use. They would appear to have been (don't know if they still are) very unique and so I would be very careful deciding which one to buy as a replacement.
Maybe email Specialized UK?
M

ok thanks for that, will give spec a try