Dont know how I originally missed this thread. First thing to do for the gear hunting is a tcu reset. That can be done with a vagcom cable, a laptop, and freessm. As for the soft shifts, the 05-07 5eat's have a couple of valve body mod options. Transgo 5eat 350z kit installed by a transmission shop or yourself if you're nuts, or the hexmods vb. Look into them on legacygt.com if youre interested.
You should definitely start off with a tcu reset.
You should definitely start off with a tcu reset.