I don't think the cold would affect it too adversely. I would not suggest controlling your engine with a carputer though, as that option would be much more unstable than the original ECU that the car came with. In fact I thought of this myself, and then realized that if Windows decided to take a dump while driving down the highway, you could be in big trouble.
If anything, your idea of interfacing it with the ECU would be more reliable, although much harder to accomplish.
I also thought of creating my own fuel injection system using a PIC microcontroller, or basic type stamp, but haven't really looked into that idea very thoroughly (sp?)