Took me picking up three supposed "E" CDIs before I actually got an "E" CDI.
To run the E CDI in the S / SM you must remove the green wire from the 8 pin connector. To do this use a small flat blade screw driver, and lift the plastic tab gently upwards (seem image below) and pull the green wire out. Nothing should need to be forced, if it seems stuck try pushing the wire back in some, and re-lifting on the tab. It does not take much, you don't want to break the plastic tab.
I didn't really notice any difference so far, so luckily I don't have much money in it. If you are thinking about switching to an E CDI, I think the money would be best spent elsewhere first.
I decided to go ahead and shorten my RS2:
This actually turned out to be a bit harder than I had planned, but overall not too bad:
The sound level only increased by 1 dB over it's stock form, but it looks much better in my opinion:
