Full rebuild ekak nam tikak loku wedak thama namuth nodanna engimak thiyenewa ta wada hondhai. Hari thanakin genuine parts dala kaloth aluth engimak gaththa wage thama.
Depends.
If head is warped - probably no point of rebuilding. if less than 0.3mm, maybe you can machine the head and use a thicker metal head gasket and get away with it.
If the block is cracked / deformed - once again no point in rebuilding.
It head and block are in decent condition (you need to consult a machinist and check for the tolerances), you can rebuild the engine.
If it's high mileage, you simply cannot convert it to brand new condition. (you will still need to run thicker oil and it may burn a little bit of oil)
If engine swapping, ECU probably won't be a major concern. You can always remap your stock ECU and probably get extra 10-15 WHP with a dyno tune + s/s exhaust + intake + EGR delete. Or even a standalone ECU (costly though)
About 1NZ block - I'm no Toyota expert, but Toyota heavily relies on the parts-bin policy (share parts between platforms as much as possible). So I assume you can find the correct engine mounts from some other model. Also, multiple heads fit on 1NZ, so if you have enough clearance, you may have the possibility of getting an engine with a better flowing head.