Buying new used engine?

Most yards expect that you can swap over parts to make it work if they are not correct. However, in looking at the parts listing for the engines they are different. It shows 4 part numbers for the non turbo version of the long block. 2 for California legal and 2 for Federal with one pair for manual and the other for automatic. Subaru parts also shows the manual engine is a different version than the automatic so I would agree with the mechanic. The part numbers are on the image I attached if you wanted to look at the engines yourself. Looking at things like the cylinder heads and crankshaft I don't see anything different though. I suspect that the manual might use some different sensors so that they are not directly interchangeable and that is why they are not listed as direct swaps in the service information, but looking at the interchange books they say that the automatic will work, you might need to swap a few pieces but that shouldn't be that difficult. If the mechanic hasn't started on it yet you might try a different shop and see what they say.

I would buy the engine, then when the one in it is out compare everything and see what is actually different. It shouldn't be anything major that needs to be swapped over as all the main engine parts are the same. It's most likely something small but in the OEM world if you change a single piece, it would get a different part number. It could be as simple as the manual trans version gets a pilot bearing for the clutch, but the automatic doesn't. Never really paid attention as most of the ones I get need timing belts or more often head gaskets and those get done in the car.

Yeah, I try to buy off local yards or ones I've dealt with before because of things like that. Hope you get a good one. Keep us in the loop please.