The hub of the torque converter centers itself on the pilot of the crank, and then its spun around to tighten it to the flex plate, If it has no support in middle when installing then the converter will sit crooked when you tighten to flex plate as the input shaft impeller inside the converter sits freely because the entire torque converter is a fluid coupling. Im amazed that the mechanic didnt see this, I have never seen a mechanic miss tha specially a gulf/ksa experienced mechanic, as 90% of the cars there have automatic transmissions. The imbalance of the TC will literally send harmonics down the crankshaft and destroy the thrust bearings and mains too. (now your flex plate warp makes sense)
btw - toyota and infact every other japanese brand temperature gauges are absolute garbage, they will stick to mid position if the temperature range is between 80~105C - they will move up a little at 125~130C (head gasket shifted) and then immediately ram to max when the temp goes above 130C. - that is if everything is going good.
well - now you have experienced this, please record this as a learning experience. Im not tooting my horn or anything - or trying to ridicule you, but in Karachi when I ran my shop and did rebuilds. All of them were factory spec top notch and nothing compromised - It was very pricey compared to every other workshop in the city but the results were good and guaranteed. I would not hand over the car unless I drove it myself for 100 kms (this is my "breakin procedure" where I literally gunned the engine under load)
Another factor which I have also pointed out numerous times in the diesel thread is overfuelling, overfuelling causes higher EGT which can literally destroy the stennite valve seats and flake off the steel valves, your pistons are too soft compared to it, It doesnt help that the cold press sleeving will be bored with "solid tight" clearance which doesnt allow for the expansion that the pistons will experience when boost hits and you get this party going on. The 2 stage nozzles are quite hard to get right without the correct tools, the 2nd stage hits when you load up the engine (turbo boost pressure present) - overfuelling would let the fire keep on going, I have literally seen pistons which looked like someone took a welding torch to them and made a hole.
btw - the engine is opened up now, but can you have a look at the timing tensioner and check for its mounting.