Results: Evaluating a Refurbished 1D
The broken viewfinder shutter is definitely a problem, and shoul've been fixed in the refurb.
That one "dust" particle is also a problem. It doesn't look like normal dust (note that it's not round). It could be a scratch. Or it could be something REALLY stuck to the sensor. That, too, isn't normal.
Those two items are why I'd send it back.
Hot/dead/stuck pixels. I've never done testing with that program you mention to actually count these. The 1D isn't known for it's ability to do long exposures, though. I wouldn't let that problem bother me, unless I really wanted to do long exposure photography. In that case, I'd go for a D60 or 1Ds.
The front-focusing seems pretty "normal" to me. Most of your screws ended up at the far edge of the DOF. If these were shot in relatively low light (indoors, cloudy/shady, etc), the results are what I'm afraid you'll find on ANY Canon SLR body. Not just the 1D. The 400/2.8 was too far off, of course.
The Unofficial Photographer of The Wilkinsons
Photography -- just another word for compromise