What it sounds like your tranny is experiencing is a bad case of gear lash. This occurs with a piston engine because the power comes in pulses and the force applied upon your gears is not fluid like in an electrical engine. Gear lash is a common occurance in cars that use lightweight flywheels due to the decrease in rotating mass and due to this decrease the pulsating force has less weight to exert itself upon. Instead of the pulse from the engine power being dispersed into the flywheel, it gets dispersed throughout the rotating mass of the three shafts in the transmission, in which there is a small amount of circumfrential play. This play increases as your transmission wears and clearances between internal contact points become wider. By not having your driveshaft connected, you have a point in your transmission that does not have any rotating mass to balance out the pulsating force from the engine and it is most likely that what your are describing is gear lash. The R series engines are very pulsy engines in their power delivery, they run very much like Diesels exempt the combustion process. That is one reason why they run so long and have relatively low red-lines; Toyota had to beef the internals of the engine to balance the pulse nature of the engine out with weight and in turn they created a very strong and long running engine. The R series engines run so long because they are over built. As for your problem, try putting a driveshaft on and you should be cool, if the noise does not go away, it may be time to build up a new trans.
