Phase 1 ej22 is SOHC and the spark plugs do not go through the valve covers. The valve covers are a funny shape.
Phase 1 ej25 are all DOHC.
The intakes do not swap.
Phase 2 ej25 and ej22 are both SOHC, both have flat valve covers with plugs that go through the valve covers. And the flange for the intake manifold is the same between the heads. The only really obvious way to tell the difference between the 2.2 and 2.5 is to look on the block where it'll say EJ22 or EJ25.