No ideas for you Rich, but your problems sound very similar to what a local guy (Drake / "cutlass") is going through with his truck.
I let him borrow my AE multiple times but he never really got to the bottom of it. I just remember him saying his miss was always worse in hot weather.
2003 F-250 XLT 7.3 crew cab 4x4
Zoodad - 6637 covered by Pete - RiffRaff AIH delete, boots, and plenum inserts - Magnaflow #17979 4" exhaust - DP Tuner F5 chip 40T, 80E, 120R - Autometer #3804 boost and #3845 EGT gauges - EBPV delete - USA ported shroud compressor housing - Garrett high flow outlet - Warn 11690 hubs