If they are both auto tranny, there shold be no issue swapping in the 2001 engine. I swapped a 2003 2.5 L engine from an '03 Forester into a 2001 OB, both were automatics and no issues. The EGR thing is your choice; you can either have the head drilled to accept the EGR pipe or cut the pipe off and have a welder weld up the cut end (so it acts like a plug) or take the EGR pipe and find a plug that matches the thread on pipe (that goes to EGR). I think you could even leave the EGR port unplugged and just disconnect the connector (so EGR valve won't open). But this would give you an engine CEL (light) for EGR malfuction for sure. I can't remember what I did for the PCV hookup but I'm sure it wasn't that difficult. Depending on where you live, it could be a struggle to get the engine and trans separated. In the salted north east, the dowel pins tend to get stuck, making it a chore to get engine to separate from tranny (there are threads on this). Also, be very careful not to let the torque converter pull out of the tranny. If it does, you need to be very careful reinstalling it (search is your friend here too).