I could be wrong but, 3rd gen 4runners have add on security systems, in the 3 and a half years Ive been at toyota, Ive never seen or heard of a security system tied to the ecm. now, I have heard that 99+ limited have chipped keys. if yours is a limited and the "new" ecm is not registered to your keys chip, it wont start. or their is always a possibility that the ecm is bad.
I just asked the master tech in my shop. He told me that if you have a chipped key and buy a used ecm, you wont be able to register the chip to a used ecm but, if you buy a new ecm, it comes in registration mode which means once you install the ecm, the first five times you start the 4runner the ecm will read and store the keys chip code