The term should not be used here until the OP starts the engine. Then he can fool around with cosmetic touch-up (resets/adaptations etc).
Bad timing (so bad it trips the CheckEngine) has nothing to do with phonic wheel (assuming it is mechanically OK, installed properly).
It (reset/learning procedure) is also NOT a way to "fix" bad timing. By the way (with bad timing +/- one tooth) engine still must start.
Real goal is to have
mechanically good timing, not fooling ECU, that timing is "better" (by using software tricks/resets)!
There is a play in the timing tools...and the phonic wheel (before you tighten the bolts)... Plus VVT (another can of worms).
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Question: which position is the correct one? Where should I "freeze" the phonic wheel (torque 3 bolts)?
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Performing a "phonic wheel learn reset" can do more "harm" than good. You don't know which way you're fooling the ECU.
Don't do it for the sake of doing it. Just because there is an option, doesn't mean you "must" use it (monkey see, monkey click buttons).