You are far from screwed - I had the exact same issue (you can read all about that
here). The thread in the post above is your solution, ask
@
Brian.
if he can reflash your ECU for you. In the meantime, you can use your A/T ECU, it will work just fine, you'll just get a few Check Engine Lights about shift solenoids not responding. Let me know if you need any help.
Edit: And FYI, the M/T ECU is not your issue, the immobilizer (which came standard on all Limited trims starting in 1999) is your issue. No other ECU will work regardless if the vehicle it came from had an immobilizer or not.
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1999 4Runner Limited - 5VZ, 4wd, Factory E-Locker, Multi-Mode, 5-speed swap, Armored, Icons, 295s (
thread)
2001 Tacoma Xtracab - 3RZ, 4wd, 5-speed (Daily Driver)
