I bought a 97 obs with 5spd swap...the swapper didn't mess with the ecu...so here's the issue while driving and Comin to a stop I usually downshift and compression brake bringin the Rpms up and when I get to a complete stop the car starts to idle rough and feels like it's missing if I turn it completely off and start it back up it will run fine again...been driving it like an auto the last couple days(while coming to a stop I just push the clutch in and use the brake only instead of compression braking) and I haven't had any issues...it is throwing a couple codes

P0170, p1507, p1722 automatic transmission diagnosis curcuit high input

P1507 is the Idle Air Control Valve and could easily be the culprit of your problem.

 

I've never done a Subie swap, but on others (like Honda's) you have to swap the ECU from an MT or always have a check engine light.  I'm not sure if a Subaru is the same, but it's something to check out.  

I too am having this same issue with an EJ22 that I swapped into a vw bus.  Do you recommend changing out the IAC valve or adjusting it?  Or is this just something to live with?  There must be a way to get the ecu to recognize it as a manual transmission.

I figured out my issue, the AT/MT identification wire was ungrounded.  

 

This article was a fantastic resource.

http://www.shoptalkforums.com/viewtopic.php?f=19&t=145631&hilit=neutral+switch