You're right - it's not Just the color - you have the analyze all the flame characteristics.
Reminds me of a little story.
I Pay Attention to what machines do: how they feel, look, sound, and seem. I really do and I think they appreciate it.
In the case of oil burners I had hours and hours and hours of tweak & study time with oil flames. At one point the subject at hand was a 15 HP fire tube steam boiler. Under my hands over time it had come to running three small nozzles at high pressure to get the output and the flame trended to blue. A helper a year or three out of school happened to be with me on that job and after I was done whatever we were doing to the boiler/burner I flipped open the sight port with a wrench, massaged the air shutter back and forth a bit to zero the look of the flame in, lock the shutter with the wrench, and flip the port cover closed. And then as I was standing up said: "That's close enough for a government job (which when I say it means 'now it's perfect <g>) - wrap it up; we're outa heah!"
"What did you just do?"
"Set the combustion air. You're supposed to be watching me."
"What about the combustion test?"
"I think we're good - I'll put the tools away; just sweep up this floor and straighten up in here."
"You can't set the combustion air like that! How do you know it's right?!!!"
"Well; I'm pretty sure - it's already dark; lets go."
"You're nuts - nobody can do that!"
"Just pretend I can - let's go."
He laughs and insists and I am laughing at how serious he is. "OK; tell you what: you go get the Bacharach and I'll unadjust the burner so you can do it right."
By the time he got back from the truck I had reconsidered: "I didn't touch anyway yet - let's get these results first and then we'll have a written record. THEN I'll scramble the burner so you can set it up better. And we'll get your results for comparison."
We do and he sets to work. I wander around listening to steam traps and so forth - the place is closed; I have a key. I forget how long we were there but at least another hour. He is outraged at himself because he can't even equal the original numbers. He declares the first a fluke and wants me to do it again.
Of course I am yawning and shrugging and casual but I really don't know if I can do it again. He fiddles with the burner and then tells me to fire it up and try again. Hit the switch, delay, lightoff, settles down to smoking, and I set down on a bucket to ease the shutter closed a bit. Flame clears up so I squint in at it, tweak for a few seconds, and lock the shutter. "OK; there you go - take a quick look so we can go."
"Oh no you don't! I want to see the results!"
Which he then found to be exactly the same as my first try. <g>
His instructors had drilled into him the use of combustion test gear. And was absolutely convinced, as he should be, but after the above episode he changed to insisting that 'no one Else' could adjust accurately without test gear. <g>
You guys sure can make me remember some fun times. <g>
PHM
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One of the first thing they teach you in the “Combustion Performance and CO Safety” certification class, is that flame color means nothing. No matter what the “youtubers” are telling you.
The second thing they teach you is if you are trying to diagnosis a combustion problem without a combustion analyzer, you are only guessing.
A combustion analyzer will not confirm that a HX is cracked or has a hole, but will give you a good reason to go looking for one based on the numbers presented to you. It will also show how efficient the unit is operating, and more importantly, how safely it is operating.
It is hard to tell from your pictures, but it looks like the issue you may be talking about is in the crossover tube between the two burner.
So I would highly suggest, you try to find a company that knows how to use a combustion analyzer as a troubleshooting tool, and take all the guess work out of the diagnosis.
