Have you bumped the timing yet? If you do, you'll probably recover most of the performance drop you have been feeling. I think you'll be just fine running the stock ECU. Open loop mode is only when you are floored. When you are just driving around, you are in what's called "closed loop" for emissions concerns.
I'd be suspect of the O2 sensors. They can cause that problem to surface. Pull the codes and see what comes up.
Good luck!
Kell