HI,
Some time ago I worked on automotive engine control in order to add a hydrogen cell (Brown gas) to the engine.
We followed two ways, modify the sensors in order to give the car cpu different value and try to re-map the car cpu (at the end we followed the first way).
I do not know in detail what modifications you want to add, but for sure I am able to do this.
no problem with freescale, and I agree to think to a fpga (I would suggest Altera Cyclon family).
Thank you in advance
maurizio stefani