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.

 

If timing marks were off its usually pretty obvious its off enough to make it run rough. That said, 1 tooth off on the drivers side cam will cause misfires because that's where it reads cam position for fuel and spark timing.

 

Incorrect cam/crank sprockets or dead cam/crank sensor will cause a flat out no-start. No difference in auto/manual sprockets.

 

My initial thought is a bad coil pack. Was that carried over to the "new" engine? Are injectors original or did they come with the engine? If you swapped them did you install new o-rings?

hand crank the cams and sprocket to their marks, do a tooth count.

 

are you moving the intake over? maybe some IAC problem?

 

can you scan for codes?