Exactly. From what I understand, the counter only tracks ignition cycles since the last ECU update. I tuned the truck about 1–2 months after purchasing it, so naturally the ignition cycle count will be high. I also assume that if Ford pushes an ECU update, it would reset that counter — so if that happens, you’d want to retune immediately afterward.
That said, can they still tell? I honestly don’t know for sure.
It’s also why, beyond the tune and exhaust, I probably won’t go much further. The more parts you add, the more attention you invite. If you roll in with aggressive springs, tuning stickers, exhaust, and a CAI, it’s probably going to raise eyebrows — especially if you’re dealing with a 10R60 issue.
I still stand by this: if you can’t afford to replace the 10R60 out of pocket, don’t tune it. I’m less concerned about the 3.0 itself. After running the ZFG tune, if you drive it in Normal mode and just enjoy the added power responsibly, and something fails, it likely was going to fail anyway. But repeated hard launches in Sport mode? I’m not sure how long the 10R60 would tolerate that — and I don’t plan on finding out.