Re: the transmission. It is an all new unit for the 987, sourced from Japan. So, history on the 986 trans will not be useful to you I think.
That said, the trans and clutch on the 986 seemed to be troublefree for the most part.
It was the dreaded RMS that many complain about.
I do agree with the comments on how the interior was redone on the 987, I did not like the direction they took on that. Of course, that is subjective.
The car popping out of second sounds to me like a bad syncro. This usually happens on cars with tons of miles on them, not a new car.
Please keep us posted on what this turns out to be.
Best of luck.