The part with Naruto meeting his dad is important because we notice that he is conscious in his own mind even before his dad came to rescue him:
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Therefore, for an undetermined amount of time, Naruto was aware of what was going on outside without the ability to control it. He was in despair because he didn't want what was happening outside to continue. The fact that Naruto actually conversed with his father while in that mode suggests that he could tell what was happening outside.
In both Minato and Orochimaru's case, the explain that they could easily see everything that went on outside simply by being within that person's conscious during that time. Therefore it is perfectly logical to assume that at this time, that being different from when he went in 4 tails mode, he was able to retain some level of conscious to the point where he was able to remember what happened, but not at a level to sustain control.
Also keep in mind that the part of him that was fighting pain, 6-tails kyuubi, seemed to be on a level of consciousness greater than when Naruto fought Oro in 4 tail mode. This time around, Kyuubi smiled at times, knew how to counter pains best tech, Almighty Push, and even knew to break the seal on Naruto's neck. The point being that some level Naruto seemed to exist within the Kyuubi at that time. Either it retained Naruto's knowledge and used it to its advantage, or some level of Naruto's consciousness still existed in order to utilize what he knew in the fight.
I think its safe to assume that in this fight, Naruto retained memories of what happened but was still not able to control it. In addition, here Naruto realized that his clones are gone and knows it was from going into 9 tails mode. I think this is reason enough to know he retained at least some level of memory this time:
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