Expecting factory warranty from a vehicle thats about 8 years old, and has surpassed the 100,000 km bench mark really is pushing the factory love. You may remember that Toyota changed the crankshaft size back in the early 80's from.. 40? to 42? mm ? on the 4AGE motor. i cannot remember the specific numbers - but they must of done this for a reason, Maybe they thought it did not have sufficient size / strength. Anyway, this friend of mine has had this MR2 from the early early days, with good service history. At 1..60? thousand kms, he was driving home one day, the thing stalled, and wouldn't restart. This particular drive car was never really thrashed, log book'ed.. etc. Motor pulled down - Turns out the crank, had snapped in half. The Crank fracture marks on the crank indicated that this had been happening for many 10's of thousands of kms. Possibly this was the reason back in the early 80's that they increased the size of the crank.
Sometimes they get it right, sometimes they don't. Chances is its just an age thing - when building & testing them, this must not of been an apparent issue that caused any need to suspect a future superseded part(s). The ECU, that is.
At least you found the issue.(s).
Brand new one at $13,*** something. Ouch. lol.