Noidea

Hi, first post here. I hope this is the right section. Got a 1998 Subaru Legacy Outback here. I bought it with a blown engine with the intention of swapping it out for a good one. The swap went well. On the block I bought I did the head gaskets, timing belt, water pump and all new valves. I started her up and it's running rougher than rough. I was sure to check the injectors, intake and the usual stuff for this issue. I chalked it up to a bad motor. So I go get and throw in another motor/heads/intake and I'm getting the exact same issue. Only thing I can think of is that the engine came from an auto, while this car is a manual. I was wondering if the crankshaft gear or the camshaft gear are different between autos and manuals of this year? The timing mark is as close to top dead centre as possible, so it doesn't appear obvious that they are different between autos and manuals. I no longer have the original sprocket off the engine the car came with as I didn't think to check to see if there would be a difference. I've worked on several Subaru's over the years and never had this issue until now. Any input or help is really appreciated. Thanks.