Filling in some gaps.
I've talked to Harrison Ellenshaw about this film a lot (probably more than he would even like to admit......) and gone through his boxes of stuff. Surprisingly, I could find a single photo of the Cygnus (or any of the models for that matter) under construction. In fact he doesn't recall taking any. He was busy with the mattes, his father was busy with everything, and everyone was busy re-writing the script. (Yes, Peter and Harrison had a hand in that, too. The zombie crewmen - Harrison's idea.)
He does recall getting a phone call one day and having to hustle down to the miniature stage to pose for photos with the Cygnus and his father. Those are the B&W photos you see in CFQ. He didn't have the negatives for those.
The surviving Cygnus model (remember that there were two) was damaged en-route to MOMA, and Disney had to send out a couple of model makers to patch it up. During the course of the exhibit, parts fell off and could be seen lying around the plinth the model was on. After it returned to the studio, Harrison recalls seeing it (decaying). He can't remember when he last saw it, but he thinks (I think he said) he saw it during TRON.
The Smithsonian rumor has been floating around for a while. Last year (2010) in fact, we heard it might be in Disney Imagineering controlled storage (separate from the general Disney Archives storage). We placed a few calls and minions were dispatched to look for an appropriately sized crate but nothing turned up. Tracing the rumor back, we had to discount it due to the non-reliability of the source (long story - lots of politics). Likely the thing is in a landfill. Disney cleared out a LOT of props and "junk" when they reconfigured the backlot and got rid of the effects stage. The Archive only has isolated parts of the Sentry Robots because all the rest got thrown in a wood chipper back then. Maybe parts of the Cygnus will show up at a future date. I'd like to think a tower had survived.
I've been through several archives on the hunt for info for Charles' obsession (Harrison thinks he's nuts. Talented, but nuts.....) and have come across only one photo - actually a piece of film from a test - that shows the Cygnus only partially constructed -
Without getting into all of the details, this image is from a test that was done in the early summer of 1977. The frame of film is from a rotoscope test (the stands supporting the model have been hastily painted out. I'm not sure if they were rephotographing a print or what. There are grease pencil marks on the left that suggest some sort of overlay. I haven't run this by Harrison yet, but I'll bet you he won't remember as he was the matte painting supervisor.
I'll try to dig up a better scan, but it's from a 35+ year old film test and it's only from this one angle.
Gene