So I just wrecked my 03 gs300 so I went and bought a 99 gs300. The thing is the 99 has no key and won't start. I took the steering column/ ignition out of my 03 and put it in the 99. Well I went to swap out the ecu and the harness is totally different. It will not work. Do I have to swap out the ecu? The car is now actually turning over just won't fire. When I lost my key months ago the dealership said the key has to matched with the ecu, but I read somewhere the 98-99 that does not apply. Can anyone help me out?

Each ECU has it's own keys programmed to it and a master key needed to make copies.You will need the ECU for the key you are using. This applies to all years as I understand it. There were changes from the 98-00 and 01-05's including the ECU/harness. So unfortunately you did not find a compatible donar car. You can swap ECU/keys and the key tumbler from a 01+ though.

Thank you! If I just took the harness off the 03 and put it in the 99 would that work?

Easier said than done. I wouldn't. Other changes were made too. Later models supposedly have changes too the tail housing off the trans with different sensors that won't work for the different ECU programming. When I bought my built trans the only thing they wanted to know was whether to send it with the earlier style electrical or later. And they would just put on the complete tail housing from one or the other. So if you do, be prepared to have to swap connectors too. And like I said, maybe the ECU wont accept the trans data and fail to work right. I'd look for another compatible year ECU/keys with the master key as well.

Honestly your best bet (read: most affordable option) here is to just take the VIN from the new car to a Lexus dealer and get new keys made. What you're trying to do will basically involve swapping over everything controlled by the ECU (read: basically everything) from the old car to the new one. Unless you've got a lot of time on your hands, that's not a very sensible choice.