When I did my 2.2 (I know it's not a 2.5) I ran into an issue with one motor having a EGR system, vs. not. Made complications snow ball into not being able to do a "great" job making the timing covers fit correctly.
My issue was using a '96 motor vs. a '98 motor. They had 2 different generations of the 2.2 during that time. I guess that is something to look at when searching. "major changes" over the production of the 2.5.
You just need to make sure that there aren't any stray sensors on the coolant crossover pipe under the intake, or on the intake that will lead you to having sensors that the computer can't control, OR sensors the computer is looking for, but you don't have.
2nd EX. Had 2 sensors on the crossover pipe vs. 1 and they were in different locations. Solution was to re-use the old one.
Subaru tends to keep majpr components the same shape, but re-arrange, add, or remove various sensors especially in the intake region.