Peter,
Interesting comparison - no suprises really.
Since were looking at primarily a H-Alpha object I thought I'd throw in some Quantum efficiency theory
The data I have on an unmodified 5D puts QE at less than 5% at H-Alpha, but then you have to remember only 1/4 of the pixels are sensitive to H-Alpha. With the red filter in place the STL11000 problably has 30% QE at H-Alpha but this is distributed across all its pixels. So we are looking at least 20x more H-Alpha sensitivity for same exposures in favour of the SBIG!
If we modify the 5D and increase the exposure to 90 seconds (as a number people are suggesting), we get a bit closer maybe to around half the sensitivity of the STL11000 in H-Alpha. Of course there are better CCD's for H-Alpha detection than the STL11000.
Peter, what I'd also be interested in though is seeing is a same exposure unfiltered STL11000 exposure versus a 5D with the red/green/blue channels combined in a Black and White image. I'd be interested in seeing difference in limiting magnitude of stars - have you got something along those lines?
Terry