You will throw a code and get the SES light, yes. Intense PCM's are notorious for doing it - it isn't necessarily a bad thing, and I honestly don't know what they do/change that is different from anyone else.
As for how/where to get a case learn - either the dealership or anyone that has a TechII or a Snap-On scanner. What needs to be run? "DTC 1336 - Crankshaft Position (CKP) System Variation Not Learned".
What does it do?
The crankshaft position system variation learning feature is used to calculate reference period errors caused by slight tolerance variations in the crankshaft, the crankshaft balancer interupter rings, and the crankshaft sensor hall effect switches. The calculated error allows the PCM to accurately compensate for reference period variations. The crankshaft position system variation learning feature enhances the ability of the PCM to detect misfire events over a wide range of engine speed and load.
The crankshaft position system variation values are stored in the PCM non-volatile memory after the crankshaft position system variationlearn procedure has been performed. DTC 1336 set indicates that the crankshaft position system variation values have not been stored in the PCM and the crankshaft position system variationlearn procedure must be performed. The learn procedure is required after the following service procedures have been performed, regardless of whether or not DTC P1336 is set:
PCM replacement
Engine replacement
Crankshaft replacement
Crankshaft balancer replacement
Crankshaft position sensor replacement
Any engine repair(s) which disturbs the crankshaft/harmonic balancer to crankshaft position sensor relationship.
IMPORTANT: Be certain that they DO NOT select "REFLASH PCM" - if they do - you will have a stock PCM....again.
-Swash