Reprogram keys?
 

Do I need the dealer to reprogram keys after replacing the ECU on a ‘99 4R limited?

There's no chip in the key on a 99, it's just a plain old dumb lock.

And no need to go to a dealer to pair a fob, but it's a quirky task to get the car into programming mode to accept a new one.

if the ECU is from a Limited with immobilizer you will need to program it as the key has a chip and the fob will also need programming aswell, a non immobilizer SR5 is just a plain old key, then you get into the USA dealer installed anti-theft under the seat, obviously you can't mix immobilizer ECU into a SR5 without a hack.

Oops, I always forget the Limiteds had more bells and whistles. Just speaking from experience on a couple of SR5's.

Back in the day if you lost your keys to the first Toyota immobilizer system 98-00, you had to get another ECU, WITH coded keys, so the OP will want to go back to the donor Limited and harvest ignition, keys, door locks, hatch lock and potentially the hatch ECU so it will work with the FOB window down option. Supposedly this system is impossible to hack and this vehicle cannot be stolen without a programmed key.. see the issue, big oops by Toyota, I’ve heard rumours that locksmith automotive pro’s now have a work around to rewrite ECU to OG ignition keys??. Hopefully the OP will update us as I’m ready to start replacing capacitors in fear of losing an immobilizer ECU and not being able to find a replacement or coded keys. I usually replace Capacitors every 10-15 years in my 1992 Mitsubishi due to it being parked causes caps to leak if not kept energized..

The used replacement ECU wouldn’t start the car, even though it was the same part #. The crux of the issues ended up being an issue with wrong in the harness, so reverting to my original ECU seams to have my keys working again.