Transmission is essentially the same for each motor, they both use the MTX-75.
The 00-07 have identical underpinnings, the frame construction on the 08-11 foci are structually a little bit stronger but they don't offer the 2.3l motor. And I think those cars may be slightly heavier as well, but I'm not 100% on that.
There is a slight variation in the shock size for the 06-11 foci, but that's the only change that I'm aware of other than stock sway bar sizes. That can easily be changed and probably would for road racing or rally anyways, so that's not much of a concern.
The interior between the 00-04 and 05+ is different, but that's a mute point with a gutted car as well. Happy modding