RRAMJET, I might disagree with you regarding the question of whether or not there was an upset condition. According to the Hess report (NTSB exhibit link below) Molin did not use the rudder during the first wake encounter, but did during the second wake encounter.
NTSB exhibit - Hess report - possible PIO
The nature of the 2 wake encounters are different for the following reasons. At the time that AA 587 encountered the first wake, it was in a left turn (previously requested by ATC) with a bank angle of about 25 degrees left. The first wake is believed to have been from the left wingtip of the JAL 747, thus its rotation was clockwise (as the pilot would "look" straight ahead into the vortex). Since the aircraft was in a left banking turn, this wake did not disturb the aircraft that much.
However when the second vortex was encountered a few seconds later, while still in the left turn, the plane reacted more severely. The second vortex is believed to have come from the right wingtip of the JAL 747, thus is was rotating counter-clockwise. Since the aircraft was already in a left banking turn, the vortex only exacerbated the left bank. Molin responsed to this by applying full right aileron, and then tried to assist the right roll with the rudder. This in turn started the rapid chain of events that lead to the loss of the fin.
So the question may be, did Molin believe that his aircraft had entered, or was about to enter an "upset condition", when the left banking turn began to roll left even more severely with the rotating vortex of the second wake encounter?