Back to the printer... I bought two new heads and replaced them which rules out the heads as the problem. I got a hold of the repair manual. Since the heads aren't the issue, this leaves (according to the manual based upon the error code) two possibilities, a malfunctioning head management sensor (which detects whether or not ink is firing from the nozzles) or a malfunctioning motherboard. I've never ever seen a motherboard fail in such a consistent and calculated manner. I've seen some crazy things before so I won't say it's impossible but, a malfunctioning head management sensor would certainly be consistent with the symptoms I'm seeing.
When speaking to support the week prior, after receiving a quote of $1400 to fix it (as mentioned before, Canon charges a flat rate, so it's $1400 for a $50 part or $1400 for $900 worth of heads, a $1k motherboard, and other assorted parts exceeding $1400 so it can go either way but I suspect most repairs won't even come close to being worth $1400) the tech mentioned "it could be anything from a $50 sensor to a $1000 motherboard". While it's not a guarantee that the head management sensor is the issue, that would appear to be the case so... $50 part = $1400 to fix. I tried to purchase the part and after getting bounced around I was told that they only sell parts to service contractors.
Out of curiosity I called Epson and asked them how they provide service after the warranty expires. They contract the work out to Precision One. It's $100 to go out to a location, and $175 per hour of work so basically a service call is a minimum of $275 + parts. When Canon sends out a contractor (in this area it's Pitney Bowes) they have to come out twice, once to diagnose, and then the following day to install parts. I asked how Precision One handled things. Epson said that they stock parts in the truck when they go on a service run and in addition, Epson gives them a list of potential parts that they think might be involved in the problem so in most cases, one visit should take care of the problem. In the past when I've had Canon come out for warranty service they were usually there for an hour but never more than 2.
Replacing the head management sensor looks fairly straight forward. With the speed that an experienced tech can get the skin off of the machine I'm pretty certain that this would be less than an hour so if this machine were an Epson, the cost to repair this would be $325 to $500.
Now, I attempted to buy the head management sensor from Canon but they won't sell it to me. I asked Epson about purchasing parts. They're not really any different there, they said the only part that the end user can purchase is the heads. Other parts would have to be purchased through a 3rd party.
Extended warranties - Epson charges $725 for an additional year (2 years total), or $1286.50 for 2 years (3 years total). Canon's extended warranties are $1225 (looks like it came down by $25 since I last checked), and $2350 respectively.
I wouldn't be quite so infuriated if Canon's repair costs weren't so unreasonable (at least in my view, am I alone in thinking that $1400 for a $50 part which would probably take less than an hour to swap out is a bit unreasonable). The fact that the machine is still so new, doesn't have a lot of heavy use, and the failure in question has cost me at least $1100 in ink only makes it that much more frustrating.
Lesson learned in terms of researching the cost of repairs. I won't say I'll never buy a Canon again but when considering the costs of repairs, consumables (ink on both of them and heads on the Canon), extended warranties, etc. the cost of ownership for Epson's printers appears to be lower over time.
For the time being, I'm waiting for a phone call. If it goes well, Canon will be doing the repair. If not I'll see if I can get the part through a 3rd party and I'll replace it myself.