Nice bike, but it's not colour coordinated enough for my taste. Red component detailing on a white and blue frame just doesn't work. If you want to use SR, then I'd have gone for the Team version of that frame which has a black, red and white colourway. Personally, I'd use Shimano on this frame, but I have OCD about the way my bikes look.
Obviously it'd be silly to get a new frame now you've bought that, but were I you then I'd put white bar tape on for a start, and replace the saddle with the white Fizik Arione with the blue stripe down the centre (or a white version of the saddle you have if you don't get on with the Arione). The Thompson seat post you've mentioned should be fine. Possibly change the chainset for a Rotor 3D+ when funds allow. Oh, and the white Elite cages with blue detailing to finish it off.
Ok, I'm going to preface this by saying that I know that you mean well, but honestly, lots of what you suggested here just doesn't jive with me. I don't mean any offence by this post, but what follows is just why this is my
bike and not your
First off, a Team R3 is simply unavailable in size 48. When I bought this bike in April they were saying that they wouldn't have them in until August. That doesn't matter anyways because the team I'm on has a blue, black, and white kit with bits of red in it (and it all goes together rather well if you ask me).
Second, I'm simply not a Shimano person. Campy works for me in all ways. Lever shape, shifting mechanism, feel of the shifting, durability, and looks...all the way that I like it.
Third, I prefer the white bike with black component look because, well, I've never seen it before on a Cervelo like this. The white bar tape/saddle thing has been done to death. This looks way better to me, and it stands out. And going with white bar tape, saddle, and cages with blue in them just seems way overdone and gaudy to me.
Lastly, the rest of your suggestions are all form over function, which I simply do not agree with. I have an SLR because of its narrow width and small profile. I had an Arione in the past and it was too big. I have the Arundels because they are super durable; I've had Elite cages in the past that snapped within a week of usage. And why would I change the crankset out? This one fits perfectly, goes with the rest of the group, and was a special order. Really no point in swapping it.
Honestly, I like this bike because not only is is functionally amazing (the main reason I went with Cervelo), but it's unique as well. I'd rather not have the red, black, and white R3 with Shamano and an Arione that every old guy out there has. This bike is different and it's staying that way