Is there a reason to abandon the stock fan control scheme? Most of the SLCs that are running LS engines are using some version of that.
My car uses a common mod that ties both fan outputs (one from the GM controller and the other from the AC) to drive both fans when either output requests a fan. It's easy to make that mod, and in practice, there is very little hysteresis, at least in my car.
If I were building my car again with the stock controller and Infinitybox, I'd do the same thing.