By breaking in the engine are you talking about primarily the cam shaft and lifters. If that's the case then yes you can run it without the drive shaft. make sure the tranny is in neutral and get some thick wire (coat hanger) and wire the yoke from turning and ankor it a little forward to keep the yoke/sleeve from falling out. Even with the tranny in neutral the output shaft will try to turn slowly because of oil friction inside the tranny but there is no mechanical connection between the input and output tranny shafts in neutral. With the engine not running make sure the tranny actually is in neutral and you can turn the output yoke easily, sometimes the shift linkage will be out of adjustment and one of the gears could be partially engaged.
