The top-exit plate that goes to the intercooler is a huge restriction. Just look at the thing and you'll see that much.
The design itself is several generations older than the Gen3 M90 that the Series2 got. The tolerances are looser. The case is also a thicker, heavier casting, which means it heat soaks that much more thoroughly, and because it'* attached to the lower intake, the intake air charge still absorbs a lot of heat from it. Even without the intercooler, I'm positive you'll still get a denser intake charge with a Gen3 M90. Basically, you're talking about going over to an older, less refined piece of machinery, with major designed-in flaws.