My experience was similar to yours a few years back, but was on the west coast to HNL legs. The aircraft went from DC10 (two class) to 747-100 (three class). My bookings showed F and I even re-confirmed them in F in the days up to the flights. But come actual check-in day, an audit had been run the night before and I was unceremoniously downgraded to C. In fact, at LAX on the outbound, my wife (no status and not that interested in FT) was lectured at length by the gate agent about "no double upgrades!" It became a major hassle to get all four of us seated together again on both the outbound and the return.

Since your legs are the transcon portion instead of the over-water portion, your mileage may vary, but I'd expect you to get nailed by the double upgrade audit just the same and end up in C.