When I replaced the engine on my 1999 forester the torque converter was not fully seated and I think I may have damaged something .The aft becomes aeriated after a few minutes of driving.This causes problems with the viscous coupler.When I go around a corner there is a clunking from the rear end.If I put the fuse in to disable the awd the clunking disappears

You said the torque converter wasn't fully seated.  Did you realize this before or after you put the engine back in & fired it up?  Did you reseat the torque converter?

Typically if the torque converter is not seated all the way and you bolt the motor up it will damage the oil pump in the transmission.

Overfilling is the usual cause of aeration of auto trans fluid.

 

This would cause slipping of the clutches because the proper pressure does not build in the pressure lines.

 

Usually a damaged fluid pump will create slow gear engagement and immediate slipping because of low line pressure. This won't last long and the pump will destroy itself, then you basically have no line pressure.