DO NOT PARK YOUR TRUCK NOSE DOWN!, that said I had water in 1, and the 2-3 well and through someone's work on this page, he came to the realization its the split plastic cowl cover seam leaking onto the top of the motor and down the breather hole in the top of the coils, the only coil dry was 4.
If it's the OEM brakes and they are going to replace them with factory, then I'm going to say don't do it, my 19 had a little over 24,000 miles on it when the brakes began to fade, swapped out the factory junk with powerstop rotors and pads, different trunk, BTW the rotors chipped a glaze or...
Thanks for this info my Ford dealer never heard of this, and I had water in 1, 2, and 3 2 and 3 were a swimming pool at least a quart of water, and like you I parked my truck backed into my drive down hill.