Hi Eric,
I myself went for a 300d over the 350d as I was told there is a slightly better noise/signal ratio even though there is less resolution..
Also went for having the baader filter replacing the canon uv/ir so I could atleast use the camera for normal daytime photography as well (using custom white balance). Pictures still come out pretty good. Also auto focus still works good with a tweak after the mod.
With just a clear window infront of the sensor you will need a uv/ir like the baader filter in your imaging train or you will end up with star bloat from Uv and IR and your images will be verrry red and hard to process.
Hope that helps...
Cheers