just to add my experiences. bigger throttle body gives a little more on full throttle but really is a bit of a waste of time - you'd be hard pushed to tell the difference. i have the same +4mm one that omi has, ian (alpina357 on uk forums) uses an engineer friend of his to add a 4mm larger butterfly to the large butterfly, the body is nicely drilled and ported to flow with it. it's nice to have a recon'd unit though, it opens very smoothly etc.
SMT6 = waste of time. Didn't work well with our AFM. I also tried to use it for a MAP conversion, this was tedious and didn't work that well.
MS is very good. I'm now running an MS2 extra which is even better. I don't agree with bmwman about the gains on a standard M42, I fitted MSNS+HR on dan318is' standard M42 a few months ago, and just running an old map of mine it feels more lively, faster with better response.
When I had my 1.8 on the rollers, I managed to squeeze nearly 10hp on factory by using megasquirt, and that's not the whole story - throttle response etc was much better.
I agree on it being a pita to get the hang of, but once you know what you're doing you can come up with good maps in no time.