Will a 2.2 from a 98 Impreza with an automatic work in a 99 legacy with an automatic. Impreza is phase 1 legacy is phase 2

Short answer: No.

The shortblock will. You can put the 98 block between the 99 heads and it'll work fine. I put a 96 block in my 02 forester using the phase2 heads and it works great.

If you've confirmed that the motor in the 99 is a phase 2 then the easy answer is NO. not without a lot of fab work. I have seen most 99s though seem to still have phase 1 motors. Either DOHC 2.5s or SOHC 2.2s which would have the head bolts on the outside of the valve covers and 3 piece timing cover.

I can't find a 99 phase 2 motor anywhere local. Would any other motor be a direct swap

If it's phase 2 - any 2000-2004 Ej25 or Ej22 should work. You'll want to swap your drivers side cam pulley and the crank pulley from the original motor to be sure the hash marks on them match the engine computer. Also bear in mind that the EJ25 is dual port exhaust and EJ22 is single port. If you swap to a different one, you'll want a matching y-pipe as well

Been reading the forums for ideas and last post may have answer. Finished putting replacing one EJ25 for another, both 2001's. 74K for 276K mileage motor. Put 6 Star head gaskets on, RMS, all gaskets new. Was careful and took my time. Now, can't get the fuel bar to energize!. Based on previous post, might need to use my old crank and left cam to align with the engine computer - did not consider that. Runs great for 1 second when I spray ether into intake - I think a good sign. New engine was bolted to AT, my Outback is manual 5 spd. The Throttle body had a different number so I used my old one along with old injectors and old harness.  Old car was running great except it used a lot of oil and had big time head gasket leakage. Going to try swapping out those sprockets! The cam sprocket looked the same, but the crank sprocket was visually different and did not think any more about it.  Anyone with specific knowlege on that please post.

You have your answer.

Change the crank and cam sensors.

 

O.

Been reading the forums for ideas and last post may have answer. Finished putting replacing one EJ25 for another, both 2001's. 74K for 276K mileage motor. Put 6 Star head gaskets on, RMS, all gaskets new. Was careful and took my time. Now, can't get the fuel bar to energize!. Based on previous post, might need to use my old crank and left cam to align with the engine computer - did not consider that. Runs great for 1 second when I spray ether into intake - I think a good sign. New engine was bolted to AT, my Outback is manual 5 spd. The Throttle body had a different number so I used my old one along with old injectors and old harness.  Old car was running great except it used a lot of oil and had big time head gasket leakage. Going to try swapping out those sprockets! The cam sprocket looked the same, but the crank sprocket was visually different and did not think any more about it.  Anyone with specific knowlege on that please post.

On the back of the cam sprocket are lobes. They may be different.

Completing thread on EJ25 - EJ25 automatic into 01 Outback Manual. Had to pull old crank pinion from the manual block. Yes, they are different lobe configurations and that is why car would not start! On the manual, took all weekend to pull the crank pinion. Best advice was tapping the holes with M8 tap and setting in M8 1.25 bolts - got that tip from one of the other Forum posts.  Used puller and put PB Blaster on sprocket while under as much pressure as I dared. Used crank bolt for the puller to push against.  By Sunday, the PB Blaster had worked down through the rust enough to break pinion free.  Strangely, taking the crank pinion off the automatic EJ25 motor took a two-finger pull. The good news though is as soon as I got it all hooked up again with the correct manual pinion, she started right up.  In summary, to change EJ25 from automatic to manual, (1) clutch assembly (obvious) (2) front crank pinion with correct manual lobe configuration (3) used my old intake manifold, as automatic was ever so slightly different and had a different number stamped underneath.  Outback is back on the road with new lease on life.