Sounds like your spec is similar to ours. We shaved a few things off our original choice when we decided to get the aero kit to keep the price of the S under £20,000 but we are happy with what we've got. May regret not getting the heated windscreen when the frosty mornings start as we don't have a garage.
We got our car done by Coopers in Worthing, partly because it was £300 cheaper, and partly because it is a nice drive down there and back and a good chance to use the car, both before and after conversion! We also felt they would do a good job as they do this all the time, but I'm sure the BMW mechanics are just as competant. I got my finance through the bank, so wasn't tied in with the dealer, either. Warranty still there, of course.
The sills were extra, I think about £70. With the aerokit, they don't replace the original sills so it looks a bit plain without something there.
Your increase in insurance sounds a bit steep. I did alot of shopping around and settled with First Alternative, who don't charge extra for the aerokit and the only increase in premium from a normal S to the Works is an increase in the excess from £100 to £400. My annual premium is only £438 and looking at your profile, you're only 10 years younger than me. As long as the aerokit and Works are as supplied by the dealers from new, alot of insurance companies don't consider them to be modifications. Norwich Union tried to double the premium when I told them about the aerokit, so some companies will try it on.
Who are you with?
As to whether you should go ahead and get this done, only you can decide, but after we spent nearly a year owning a Cooper that we hardly ever drove, we are so glad that, despite the extra cost, we now have the car that we really want. If you're not buying it just as a car to get from A to B, you might as well make it as fun as possible. Toys are for playing with.
Having said that, if it was totally my decision, (not having to take in to consideration my boyfriend, who after all is paying for it), I would probably have been happy with the S as it was, pre-conversion, compared to the Cooper, but then again, when I put my foot down and it takes off..............