If you're looking for peak performance then do the airbox mods.
If you're not riding in sandy or very dusty conditions you might just consider removing the airbox door, rather than cutting holes in airbox or other destructive options.
Just to be clear - an EFI unit like a Power Commander 5 or 3, or an FmF type unit does not replace the ECU.
They work in conjunction with the ECU.
Not sure what you mean by stock ECU is in a box.
I'm not aware of replacement ECU's other than OEM factory Yamaha replacements.
Pictures are worth a million words here.
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2008 WR250X
Gearing: 13t - 48t
Power Commander 5 / PC-V
Airbox Door Removed - Flapper glued - AIS removed
FmF Q4
Bridgestone Battlax BT-003rs