Sorry. This was/is an evolving situation as I got more responses and information from the dealer, Toyota, and the insurer, so I appreciate everyone’s help.
I’ll reiterate that at this point you need to put on your lawyer hat. A bunch of guys on the internet are not going to change the dealership’s mind. The dealership knows that water ingestion is not the only way to bend a rod. They also know that warranty work is not as profitable as non-warranty work, and are clearly trying to avoid performing their contractually-obligated warranty service.
What we say about the cause is immaterial. It’s not on you to prove that you did not violate the terms of the warranty, it’s on them to prove that you did.
I’m betting that a letter signed with your name followed by Esq will make them reconsider whether they really want to play games with you now that they know you’re an attorney.
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If the dealer returns an engine to the manufacture with a bent connecting rod the warranty claim will be denied. Connecting rods do not bend without an outside influence.
True, but that outside influence does not always have to be water. As has been noted above, sometimes they can bend because of other things going wrong/falling off in the cylinder.
It is not the consumer’s concern if the dealership and the manufacturer fight over a warranty. That’s between them. The consumer’s involvement begins and ends at the text of the warranty, which very likely does not say “any bent rods will be denied because reasons.” 
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That would cause a lot of damage to the piston. I believe it was stated that the cylinder was inspected with a borescope. We don’t know if the vehicle’s owner viewed the cylinders in person, it may have been confirmed by the owner and insurance inspector that the piston does not have any damage.
I only saw a suggestion that it be inspected with a borescope. But it’s certainly possible I missed something (not taking the time to scroll through 100+ posts atm).
As long as we’re relegated to WAGing, here’s mine-
The staining in the intake is from someone spraying starting fluid, throttle body cleaner or some such product into it previously.
Assuming the bent rod is real, it came from leaking injectors. This also washed down the cylinder walls of the two cylinders with low compression. A wet compression test and subsequent running has since restored the compression to normal levels. The evidence has quickly vaporized. I think liquid gasoline in tbe cylinder is more likely than injesting water from an external source. Intakes are designed to avoid water injestion, it takes extraordinary situation for that to happen. IMO.
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I was going to stay out of this discussion from here on out but like a cat curiosity always nags at me non-stop.
Another cause for a bent rod is a botched oil change. Say someone overfilled it, hit the starter, and within seconds the engine hydrolocked because of motor oil. I have seen this a few times and in one instance it did bend a rod. In another instance it did not but the engine was locked up tight and this engine was a diesel.
Regarding TwinTurbo’s dead-on comment about washing down cylinder walls I have also seen that. A lot porter whose job it was to make sure every used car would start on a cold morning loved Ether. One day the boss sent a Dodge Ramcharger back for a no-start and it had been firing right up every morning.
The Dodge smelled of Ether and the engine had fuel and spark but would not even cough.
So I removed the spark plugs and ran a compression check. All 8 cylinders were 60 to 105ish. A healthy shot of motor oil into each cylinder followed by retesting compression and all numbers jumped up to 180 or so. Reinstalled plugs and the Dodge was never a problem again; especially after the boss forbid the guy from ever touching a can of Ether again. IMO Ether has no place on a car lot anyway.
Care to share the status? You have our attention and we are interested in your progress.
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We’re moving the HL to a private mechanic for a third opinion. A Toyota field rep is coming out to assess it next week. If nothing conclusive and lower cylinder still indicated, we’ll have the engine taken apart at a different dealer.
The idea that a bent rod equals water intrusion equals warranty claim denial (when all the evidence points to no water intrusion) is absurd. I don’t know much about engines, but I do know a bit about proof standards in court. To defend a warranty claim based on outside influence or consumer misuse, the burden would be on Toyota, not to prove that a rod was bent, but to prove that it’s more likely than not that water intrusion caused it.
Do you mean an independent shop . . . ?!
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Toyota does not come across very well to me even based on their comment that the only thing that will bend a connecting rod is water intrusion. That is absolutely not true.
There’s also hydrolock from excess motor oil, foreign objects inhaled into a cylinder, and now and then an engine can hydrolock if a cylinder gets too much fuel in it. E.G. the engine will lock up due to gasoline.
The latter was a common problem with CIS injected cars and I would not be surprised if db4690 hasn’t run across that a few times.
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Well as you know you can do whatever you want now regardless of what Toyota says. Then when it’s apart you can make doubly sure to document the findings and allow Toyota to also see the insides. Then you can pay for it and tell Toyota (oops Toyota and the dealer) you will meet them in the court room. If you have to put a new short block in, probably best to hang onto the old one for a while.
Good luck. It’ll be interesting to actually see if the rods are bent.
Bullsh**! I can remember certain engines, which were known to have defective lower intake gaskets, and that sometimes these gaskets failed in a big way. Coolant could leak into the cylinder(s) in large enough quantity to cause oil contamination, cylinder wall damage, bearing damage, perhaps even hydrolocking the engine. If that occurs, does the manufacturer magically get a free pass on its warranty commitment?
The 2GR-FKS engine does not have coolant passages in the intake manifold and the engine oil is not polluted with coolant. This engine is less than 2 years old, should it have leaking coolant gaskets?
That’s but one of the many problems with the CIS system 
Are you thinking about various older GM V-6 and V-8 engines . . . ?
At one point, we had a ton of GM vehicles with those engines in our fleet, but many of them have been retired by now. Anyways, I don’t recall running into any that leaked so bad that hydrolocking occurred. But there were a few that did have bearing damage, because the problem had been neglected for too long
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Under our state’s lemon law, to overcome a statutorily valid claim, the manufacturer will have to show that an “accident” (water ingestion) caused the engine to fail. The bent rod may be a symptom of water ingestion, and a symptom may point to a cause, but it doesn’t prove the cause. If a bent rod was excluded under the written warranty it would be a different story, of course. Indeed, if Toyota intended to deny warranty claims anytime there was a bent rod, it should have excluded it as a basis for a warranty claim.
At this point, there is zero evidence of water ingestion other than a purported bent rod. But this raises a question: if the engine is taken apart for further diagnostics, will there be internal evidence of water ingestion, even though there’s no external evidence (dry and unstained air filter, no water in air box, etc.)?
The key word here is “purported” . . . I believe the dealer and corporate have not (yet) made their case
If they’re going to deny you based on a bent rod, it seems to me they should prove it
Right now they’re just speculating the rod is bent
They might be right, but they haven’t proven it yet
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What does your 3rd party independent shop have to say at this point . . . ?
He’s reviewed the diagnostics and pictures and feels the same as everyone else; something doesn’t add up. Toyota field engineer is resetting the DTC and starting diagnostics from scratch this week. We’ll be there and videotaping the whole thing. Will get the HL to the independent later this week.
I asked this question earlier, but I’m wondering whether water ingestion, if it happened, will be evident when the engine is taken apart.