no, it wasnt the same as the day he drove it off the lot.
but alot of guys will say their ride is stock even though it maybe has a catback, or maybe he's running a set of drag radials or something.
a stock HD would have a very hard time running 13.6. it would have a hard time running in the 13's. 13.6 sounds like a good time for a stock lightning with an ok driver.
most likely he had a pulley and figured nobody could look and tell the difference, so he just said it was stock. did you hear a considerable whine? if so, he had a different pulley.
the harleys have a 340 HP rated motor which is supposed to run 2 less pounds of boost than the lightning, 8 vs 6 stock. as one person said, this is accounted in the pulley size.