Outback 2.5 to 2.2 and Auto to Manual

So, long story short I decided to take on a massive project of swapping a 2.2L with a 5 speed manual from my 96 outback into a 97 shell Outback shell that I had that used to be a 2.5 with an automatic. Since I had the 97, and my 96 was totalled I decided it was the best thing to do, and I was reading that the 2.2 to 2.5 swap is no big deal. Now I got it all together and it runs, and revs smoothly and everything, but when the car is idling it misses very badly and hte motor shakes. Now I see that you must match the motors with EGR and non EGR. And it seems like the Autos came with EGR and manuals do not. My 97 2.5 had an EGR but my 96 2.2 did not. When I did the swap, I swapped the main engine harness, used all of the 2.2 stuff, and the 2.2 ECU. Now is my idle issue caused by my lack of EGR? Should'nt it work fine since I have the 2.2 ECU in it and it wouldnt be looking for it anyway? What else could cause it to shake so bad when idling and then rev fine? I've gone over all my connections several times now, checked plugs, wires, all that stuff and everything seems ok. It just doesnt want to idle smoothly.

EDIT: Kind of posted this in the wrong spot.

Edited November 1, 200916 yr by Gsir08