So its a 2003 Forester with a NA Ej25 and automatic.  I just put in a low milage EJ25 NA  motor (60 000 miles) that had new head gaskets installed by the previous owner. I have no way of verifying the true milage of this motor as I just bought it and took the person word for it.  I put it in my forester and used the intake from the forester   and the motor surges up and down about 400rpm . It does this in park idling, and also under load while driving. I cant see any connections I missed. Any suggestions.  Thanks for taking the time to read this. 

I would bet on a vacuum leak somewhere in the inlet manifold system.

Or timing belt is off a tooth but that should not result in surging.

Ok thanks. I will check it out. Problem also seems to be a bit intermittent. So its a tough one. 

 

yeah, triple check all vacuum lines - if any are are "hard", replace them.