Did you test the fuel pressure when it was puffing black smoke or otherwise acting up? Puffing black smoke sounds like it is running rich, and it sounds like it might be intermittent. There have been many cases where the FPR is sometimes regulating correctly, but then will suddenly get stuck closed and fuel pressure spikes, and you won't see this unless you are testing the fuel pressure when the problem occurs.
I might pull codes just to see if there is something useful stored in CM.