Ford 80-bit programming is actually very simple to troubleshoot!
Always be at the latest firmware.
The programming procedure is the factory key learning procedure. When you cycle the first key a third time, the door locks on the vehicle will cycle (on most SUVs and Pick-ups), this is the vehicle confirming to you that you have allowed the vehicle to enter programming.
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You should be able to this without the bypass even connected.
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If the door locks do not cycle, it may simply be timing (either going to fast or too slow) when cycling between key1-key2-key1
Here's some other pointers:
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When the first key goes on, All three LEDs will turn ON ( Red, Yellow, Blue)
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When the second key goes on, only the Blue and Red should be On.
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if the yellow LED is still on when you put the second key On, there;s an issue with Rx and/or Tx
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it's also possible that EVO-ALL is actually keeping ignition On even though you turned the key off. Just do the programming without connecting the RED connector to the EVO. Reconnect it once programming is done.
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When the first key goes on the second time (step 8), door locks should cycle
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this is the vehicle confirming to you that you have entered programming
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you should be able to allow the vehicle to enter programming following the Key1-Key2-Key1 procedure without the EVO even connected.
If not using a T-harness, double check the Rx and Tx connections. Rx on the vehicle is always in Pin 4 at the transponder connector. Do not go by color because some vehicles actually swap colors, go by pin location. I've seen this enough to not trust the wire colors for Rx and Tx on Ford (specifically F-Series).