Transmission is the A340E, which is relatively common in a number of Toyotas (The Soarer, for example). Naturally, there are differences in case size etc, but the "innards" are similar.
One thing these transmissions like is being cool so it's always a good idea to fit an aftermarket transmission cooler (which I will be doing to my own car as it nears road-readiness).
As for your noises, I would not be encouraged; however you should probably get a specialist to check it over...