did a bit of the research and i think i found my problem: i conected the eccs relay (or the efi relay, as its named in s12) the other way around. I didint pay much atention to the fact that in the s12 this relay is controled by the ignition switch, but not by the ecu, so i ended up conecting the main ecu power into the relay control pin of the ca18det ecu, no wonder it fried.
Another thing that i noticed is the fact that there is no ignition coil relay in the s12, but i have no idea if this is a problem, because i did have a spark just before the ecu fried.
Now about the differences in the engine bay harness i dont have much exact information, because im still waiting for a full fj20 manual, but one thing for sure that the wire colors dont mach up at all (maybe except for the water temp sensor), also the fj20 does not have a o2 and a detonation or knock sensor, also no neautral switch.
Oh and in my s12 there is no under dash white plug, the only place where the efi harness connects to the main harness is two white plugs (one consists of only 1 pin, has to do smth with powering up the original ecu) under the afm i guess (too bad that i dont have a pic, but these plugs are the first ones on the efi harness after the ecu).
One more thing, in the write up at the first post, it is said that the brown wire on the ca18det harness is for the o2 sensor, but in the diagrams that i have it says that this wire goes to preasure regulator control solenoid valve (whatever it is).