I just finished the swap of a 2.5 dohc from a 98 forester into a 96 imprezza wagon with a 2.2 that had bottom end problems. 

At start up the rpms immediately shoot up to about 4000. 

I used the timing cam and crank sprocket from the 2.5, intake and intake wiring harness from the 2.5. So a complete drop in. 

I tried changing both the tb and iac off of the 2.2 manifold, no change 

The 2.2 did not have egr, the donor does, I removed the tube and plugged both ends and installed a solid plate between egr and manifold, and plugged vacuum hoses, not sure what I'm missing here, vacuum lines are slightly different but I think they are correct 

you've got a vac leak somewhere

Sure the EGR plate is sealed?  Intake manifold to heads?  TB to the intake?