My 99 has 2 upstream sensors as well and noticed the same issue, but if I ran in open loop, it would load up at idle. I'm planning on leaving off the downstream sensor as I've read that it only monitors how effective the cat is.
Does your harness have letters on the O2 wires? Mine has L,R ( maybe 1 and 2, it's been a while since I've been up under the car ) on the upstream wires and nothing on the downstream wire. It's like a wrapped label on the harness side close to where it plugs into the sensor...oh, you are running a different ECM, but does the harness have 2 upstream O2 plugs?