A clue might be your need to re-sequence the injectors for your cam. If you have done this, you need to do 1 more thing.......
I had the same problem on a 302 that I converted to factory fuel injection. After re-sequencing the injectors, it just seemed flat, and idled a little choppy. After doing much research on the system and talking with Hank Dertian (head engineer) at Ford, I found the left O2 sensor controls the left bank of injectors, and the right does the same for the right bank. After re- sequencing, it really screws up the controls- and the banks start fighting each other.
I asked Hank what I could do, and he suggested soldering a wire between the two SIGNAL wires coming from the O2 Sensors, near the connector for the computer. This will allow the computer to read an average of the two sides. I tried it and it worked!! It ran much, much better.
I hope this helps!!
82 Mustang GT -Ford Racing Boss Aluminum Block 347, TW Stage 3 by TEA, Ultradyne cam, , 30lb. inj, DC&O Stack Fuel Injection System, 1 3/4 Hooker long tubes, Tremec TKO II, 9" w/ Detroit Locker 3.25, Full Griggs, AKT LOGIC wheels