used the AE111 box, it was a 5-speed C56. Use the 20V shafts, they fit straight into the ae92 hubs and are of an equal length design and help to prevent torque steer, I'd post a link to the thread detailing that swap but the www.twincam.org forums are down at the moment with another MySQL error...
The ae111 will come with a C56 if it's a 5-speed, an ae101 will come with either a C52 or C56 depending on it's age. Both boxes are far superior to your C50 attached to the 4afc.