[Thumbie]

I agree with everything Reddevils7 said (except for his choice in football club). It's a lot of work, price isn't too high.
RB and TA quotes seem a bit high. Body work seems reasonable if it's done at a quality shop. Amp replacement seems cheap but if you have the budget there are better ones for closer to $1k. Bimmertech's lightwave amp seems to be pretty awesome (assuming you have individual audio package). Depends on how much you care TBH since factory is pretty decent. EDC modules are $900 new or $150 used so I'm assuming that's for a used one (which is fine).

As far as shops, I see you are also in the bay area. There are a few m-focused shops scattered around, and I would trust any of them more than a dealership.

I go to Vt Motorworks in Pleasanton, they're pretty renowned as one of the best.

Edge Motorworks in San Ramon is great too, I have some friends with e90s that go there (I might switch to this one since it's closer).

Performance Dynamic in Mountain View is the place to go on the Peninsula, have some other e9x friends that go there.

There are others, but those are the three I have personal experience with.