Mustang P0135 Crank position sensor not learned code present AFTER RELEARN?

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Hi, I'm having a problem ever since I picked up a junkyard 2012 3.7L v6 engine and installed it in my 2011 3.7.
The new engine was an automatic, so I swapped my flywheel and clutch over to the new engine so itd work in my manual.

I understand this requires a crank relearn or the misfire neutral position relearn procedure or else it might misfire under load, I have successfully relearned my crank position sensor according to a popup that comes up after the procedure, however I still have a CEL for P0135 crank position sensor needs relearn!

If I run the HP tuners DTC check with the car running I don't get any DTCs, CEL is still illuminated though. If I run another bluetooth scanner for DTCs I get p0135 still and if I clear codes it blinks the CEL and stays solid again with P0135.
missfire check is enabled. I bought this car used with a borla exhaust and it has a drop in air filter but as far as I know there is not a tune on it.

I have tried swapping my crank position sensor with the one from the previous 2011 engine and checked wiring and everything looks good.

The car DOES NOT MISSFIRE. I had some misses immediately after install before any relearn procdures, but I have put 1600 test miles on it after a relearn and it goes to redline fine in every gear up till speed limiter and and does not miss once, but id like to play it safe and figure out the cause for the CEL.

Any tips? help is greatly appreciated because i am very new to tuning. I bought HP tuners after i put the engine in to first off fix this issue, then learn to tune later on after a driveshaft upgrade.

[Nxbusa]

I've had that happen before and used an IDS to do the crank relearn and then all was good.