From what I have read there are no common or known issues with the manual. Anyone have input otherwise?
Not quite. The 2nd gen is an RA60 (Aisin AY6) that has no pilot bearing in the flywheel to support the input shaft and friction disk. It relies on the snout of the transmission and an interesting pivot to locate and operate the clutch release bearing. This by itself is annoying because the bearing doesn't move quite perfectly straight into the pressure plate release fingers and actually rides slightly on it all the time.
So it spins constantly and causes the bearing to wear faster than traditional designs and the pressure plate fingers get a groove worn. But the biggest problem is Aisin/Toyota made the extension from aluminum and the bearing race being steel means it wears a step that hangs up the release bearing.
This is an example of that the extension looks like and how it wears out:
My release bearing was toast at about 80k and it had worn enough of a groove on the snout that I had to put a Speedi-sleeve on it with an oversized bearing.
This is what the pressure plate fingers looked like:
This is the release bearing kit I used:
The transmission itself is solid. The only complaint I have would be the gear ratios are kind of odd. It has 6 gears but only one is overdrive. But really the only "problem" is the release bearing situation.
In the 2016+ sticks Aisin/Toyota went to a RC62 that uses a different design with a steel release sleeve...