Hi,
I'll go with a comparision by somebody that knows what he is doing, i.e reknown astronomer/astrophotographer Christian Buil at:
http://astrosurf.com/buil/400d/400d.htm
To save translating and reading through the graphs, it basically states that although the 400D sensor has smaller pixels, this is partly offset by better efficiency converting light (i.e the 400D has higher Quantum efficiency). The AA-IR Filter seems to stop a little more red light unfortunately. There is a little more dark noise (i.e long exposure noise) in the 400D but no electroluminence glow. Overall the 350D is the prefered camera for astrophotography, but the difference is fairly SMALL.
So Shane the 400D is still a very good choice and keep in mind you have a better camera body design in the 400D as well.
Terry