Thanks for the advice, I'm an EE major myself so I also find it to be unbelievable for the ECM to simply fail like this (all fuses and wires are okay, power supply to it is okay).
But I still followed TRDCal(thanks!)'s advice to get a used ECM since I could later return it to the Ebay seller anyway if it doesn't seem to fix the problem.
Good news is that after they putting it in the 4runner cranked and started, and then died.
The dealer said that it was the immobilizer killing the engine and they need to short it for 40 minutes to reset the ECM so not everything could be done today.
Hope everything would work out tomorrow and thanks again for all that helped in the thread!