FWIW i just swapped my busted EJ253 in my manual trans car with one from an auto trans. I've no idea about the older phase one phase two stuff, but i can say that it was simple as beans to swap a clutch onto the auto engine. Also, there were some other minor differences, you can always read my thread about it (it's in this sub-forum).
my only concern for you would be that the engine plays well with the ECU. I think a dealer should be able to answer that question.
this was my first ever engine pull and my brother and i found that pulling a subie engine was crazy easy and so was putting it back in. It took us 8 hours total, but some of that time was cleaning, and we also changed the t-belt on the new engine. also there was time lost due to me needing to help out with my 10mo old. Don't fear the mechanical work.