Interesting (frustrating) transmission issue
 

I am a first time poster, so please forgive my "lack of street cred" on this forum, but I am at my wits end here. This is gonna be long, you might wanna grab a Snickers.

I have a 2008 Mazda 5 with about 142k miles.

• Several weeks ago, my wife was driving the car and heard and felt a loud clunk and the AT light came on. I suspect it went into "safety mode" (not shifting up to top gear) and I suspect the CEL came on, but she didn't notice as it was in town near the mechanic. She immediately took it to a shop where they read the codes which said the TCM as bad, so we had it towed to a transmission shop. The guy said "a bunch of codes were set". He checked the wiring and then replaced the TCM (~$700 total).
• I drove the car the first few days out of the shop (~20 miles) and it was ok. The wife took it on a longer trip and after about 40ish miles, same thing happened: clunk and AT and CEL on and it went into safety mode - would not shift to top gear (4th or 5th). She parked it. I took a look at it later that evening. The light were still on but the car shifted just fine, all the way up to 5th. We had a code P0753 - "A" solenoid and something about the antilock system. I reset them since the car was running fine.
• I drove it a few more days with no issues and the BAM, it did it on me: clunk, AT and CEL, P0753, safety mode. I took it back to the shop.
• The guy replaced the solenoid and said that as soon as he reset the P0753 code, it set again. He deduced that it wasn't the solenoid, but that he got a bad TCM, so he replaced that. He said he drove it some and it was fine.
• I recently picked it up and went about 500 feet and BAM: the clunk, AT and CEL lights, P0753 code. It is now parked at a different mechanic.

I am thinking this isn't a transmission issue per se, but some other root cause that is making the car think it is a transmission issue. So I am including some back story:

1. Several years ago, maybe around 60k miles, the wife noticed the AC not working well. We took it to a shop and they said that a temp controller(?) had gone bad and allowed the car to overheat - I did not get a good, clear story (my fault). They said that the engine did not appear to be damaged. I asked if anything else should be checked as a result; he just shrugged. I should have known better.
2. In 2015, the transmission went out at ~81k miles. The fluid was black. I am sure the overheating cooked it. I shoulda known. It was replaced with a tranny with 87k miles.
3. Several years later, we had CEL turn on with a code showing something about engine temps - I think too cold. Two possible fixes: temp sensor or thermostat. We replaced the temp sensor (cheaper): problem solved. Less than a year later, same CEL code. Replaced the thermostat - problem solved. Less than another year, same code, they wanted to replaced the thermostat again; I said no. Took it to a dealer; the kid said it was likely air in the system, and that he "burped" it. Code was reset, no issues, I'm skeptical. A few weeks later, CEL again, I reset the code. It hasn't come back. That was over a year ago.
4. More recently, we had new break pads put on the back wheels and the rotors turned. I noticed a clicking in the wheels; took it back. They didn't put the correct clips on. No issues after that.

There are no other issues with the car. The engine runs fine; the tranny fluid is red.
I would think that if the "overheated" engine caused the problem, it would have surfaced before now, unless it heated a mechanical part and thereby shortened its lifespan.

I am wondering if the "clunk" that we hear and feel is something (perhaps brake related?) that is causing something mechanical that is, in turn, causing the code. I know it seems like a reach, but we have already addresses the easy, obvious stuff.

I wonder what was the cause of a "bunch of codes" and then later antilock + A soleniod then just A solenoid.

Thoughts?

One more question: Anyone want to buy a 2008 Mazda5? :D