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I really doubt that the problem is the PCM (ECU), that is the least likely thing that would cause these codes. The causes will take a factory manual and good test equipment that can read live mainstream engine and sensor data.
This is an (almost) impossible task. The immobiliser ECU which reads the key communicates with, and is controlled by, the engine ECU. It's not possible to just "bypass" the system. I said "almost" impossible because with the right tools, knowledge and unlimited time it may be possible to capture the code of a useable system, then design and build a black box to respond correctly to the engine ECU, which would allow engine operation. If you have lost your only usable key, you need to order a new one (as you haven't indicated your exact model, I can't give you the correct part number - keys are different depending on model/engine). You will also need a dealer who can programme a new key to your existing vehicle. If your existing vehicle has problems with the immobiliser, you may be able to find a Toyota dealer to interrogate your OBD to see what the issue is. If not, replace the key transponder unit, then the ECU. I've assumed you know it's an immobiliser issue, and that you've done the usual wiring and fuse checks etc.
There is a way to test the ecu to see if it's working properly. Go to a different mechanic and ask them to test the ecu.It is also possible that the icm ( ignition control module) is faulty. When an engine is changed out, especially with a used engine, the ecm is bad and /or your old distributor was used and the icm burnt - this is not uncommon and may not be by fault of your mechanic. A special scanner is needed to test these components.
Radio code has no bearing on the immobiliser at all.
Normally it is down to the key not recognised. Are you using the same / usual key as before? If not then try original or another key as it may be the transponder in the key you are using.
If same key or no joy then remove the lower Black plastic steering cowls on the column (normally 3 or 4 screws) you will expose the barrell assy, on the end of this you'll see the transponder pick up ring. Disconnect from loom, apply silicone grease to pins and reconnect then try starting.
If still no joy, disconnect positive terminal off the battery, touch the lead to an earth point for 2 to 3 seconds to defuse and reset ECU, reconnect and try again.
If still noy joy you will need a garage as special reading equipment is required.
It has nothing to do with ECU and immobiliser even if you turn your ECU OFF your car will start and will your but not properly without CPU your car will work in emergency mode. try finding Idle sensors and check them if they are ok
I wouldn't have thought the ECUs would be interchangeable due to the immobiliser. Thinking about it, a fault with the immobiliser would cause the lack of spark and noid. I know they usually also disable the starter motor as well, but a fault would change the way it responded.
I think a computer is needed here to live scan the ECU and see exactly what the little blighter is playing at before you go to the expense of an ECU.