500mm vs 600mm?

Wow, reading your position is like reliving my decisions. Last year, I too wanted similar things for similar reasons (nature/bird shooting). I was using a 400 DO, and wanted two things... more reach and better performance with the extenders. That left a few options on the plate, Sigma's new 500mm and Canon's 500mm and 600mm L's. I also considered the 400 DO II and the 800mm, but ultimately decided against both due to the versatility of the others.

I tend to shoot on and off a tripod so I wanted a lens that fit the need. While the 600mm is, IMO, that better glass it would be tough to hand hold for any useful time. Also I found the seasonal birds I shoot would be very tough with the 600mm. Hand holding a 600mm to shoot terns diving 40-60 feet away would be a nightmare. So I decided to hedge the bet and go for the slightly smaller and correspondingly lighter 500mm. The difference from 400mm to 500mm was greater than I'd originally thought it would be. A big plus.  The IQ improvement was astonishing, I liked the 400 DO, but the 500mm L II is on another level.  Note, if you choose the 600mm L II, I think it's a little better yet for outright acuity.

As far as Canon direct refurbs, grab one if you find one. I have number of lenses from them and they carry a 1 year warranty and generally go at the price of a used copy. They arrive looking brand new in an odd box. The only sign that they are a refurb is a red dot on the lens mount.  If for some reason you think the copy you get isn't up to snuff, you can send it back and ask they refund you or get it right. When I was looking there was an 800mm L in Canon's inventory, but the 500 and 600l II's hadn't been in inventory for more than 2 years.  I guess they just don't get returned as flawed very often. So the likelyhood you'll find one is very low.

Good luck on determining what's best for you, but from what you've said I'm assuming you should go with the 600mm. That's of course provided you don't mind being limited to a tripod for 80% of your shooting.