Replacement Engine Problems Options

[Ben_RAV4]

Hi All,

I am new, and need help to understand something. I run a 2003 RAV4 Cruiser (195000km on the clock). Last major service was done at 168000km, and unfortunately bad things happened and I had to replace the engine with a second hand engine with only 65000km on it. I picked up the car, it was running fine. After 85km, I noticed a periodic sharp drop in power and then return to normal (within a second). This started to happen more often over the next 15km, and the check engine (yellow engine) light started to flicker and go out. Then the light stayed on longer, and finally the missing in the engine got so bad I pulled over and had the vehicle towed back to the mechanic to get it fixed. Before it was towed, I noticed a red fluid in parts of engine bay, and a small pool under the vehicle.

The mechanic once he had a look is telling me that there was no fluid leakage. He says the computer management system in the RAV (automatics only) is smart enough to know when there is a new engine in the car, and that this has led to electrical issues resulting in what I experienced. They are now getting an autoelectrician to check it over. The work done to replace the engine has a 6 month 10000km warranty, and I am worried they may try and invent a reason not associated with the engine replacement that exempts them from any expenses to fix the vehicle. I need to try to understand the truth and what is and isn't plausible.

My questions are:
1. Is the electrical / computer-based engine recognition thing a plausible scenario? Why wouldn't the electrical / computer system have had an issue from the start? It seems strange this would emerge after 85km of running fine.
2. Given the yellow warning light, if the mechanic didn't install the engine correctly, what may have led to a an automatic transmission problem? Do the symptoms I experienced sound like an automatic transmission problem or the electrical problem above.

3. Has anyone ever done an engine replacement in 2003 RAV4 Cruiser Auto and experienced this issue?

Thanks in advance