if you already have a 2000 si harness, ecu, and engine, then yes it makes more sense to me to just use the si parts.
I have an EM1 that I drive daily and I love it, b16a2 is the way to go or at least one way. I've driven a variety of different hondas and have yet to find any engine with as much guts to it as my 00 Si. (hoping my h2b swap will raise the bar a bit though!)
Anyways someone correct me if I'm forgetting something but I see NO reason you couldn't just swap out the whole setup.