Diesel Bombers - A Duramax ate my wrench/ FCA/ P0089/ P0193

My mom's truck started idling rough with a P0089 code. Using my oscilloscope, the PWM pattern going into the FCA looked PWM-ish and the rail pressure sensor signal looked valid; at idle I could see the pressure dip momentarily whenever the idle dip.

I decided it was the FCA on the back of the CP3, so I ordered one and changed it.

First, when I had the thermostat cover off, the front thermostat stayed in the cover and I managed to drop a small 1/4" wrench down the hole. It looks like that hole goes down a steel tube, through a flange, then down to a big hose that loops under the engine back into the radiator. I rodded out the steel tube, took off the big radiator hose and looked through the flange that connects them, but I couldn't find my wrench. Is my schizophrenia getting worse or did the wrench go somewhere I didn't look? I believe with all my mind that the wrench fell down the front thermostat hole, but everything I believe is routinely proven to be wrong and I don't have much faith in my memories anymore. I don't see where else it could have gone after it fell down that hole?

Second, when I put the new FCA in the pump, I had to compress it in by tightening it odwn with the three screws that hold it in. Is that normal or does it mean I used the wrong FCA?

Third, after I got the new FCA installed I took it for a test drive. It now idles smooth, but when I put it in neutral (2001 automatic) at freeway speeds the idle stays at 2000 RPM instead of going to the normal ~600. It's also slow and smokes lots of black under acceleration, and now I'm getting a P0193 on top of the P0089.