Welcome!
I'm not sure how much I can help with your exact problem, but I do know that all Limited 4Runners 1999+ came with an immobilizer. When I swapped a 5-speed into my 1999, I had the same exact problem you're having, crank but no start. Turned out the immobilizer in my ignition was mismatched with the new M/T ECU, I had to get the new M/T ECU re-flashed and program my keys and it worked.
From what I understand, it's the ignition system (not the ECU) that keeps the vehicle from starting - meaning the ignition reads the coded values in the chips in your keys, sends that to the ECU, the ECU sends back the decoded value, and the ignition checks that value and then lets the vehicle start. If you put an ECU in your vehicle that came from an immobilized vehicle, and the ignition system is from a non-immobilized vehicle, it should run like ORS says. If you swapped over the immobilizer-ignition system, that there is your problem and you need the master key to start. If you don't have that key, get a local locksmith to re-flash the IC900 chip on your ECU to get your ECU into re-programming mode, and you'll need to program new chipped keys. I can get you more details on how to do that if that turns out to be your problem.