The only way to fully diagnose or rule out navicular is an MRI. My grandmother's TWH mare went through everything short of the MRI's and the permanent nerve block to deal with what they thought was navicular, and it turned out that she had laminitis, and had had it for years. Fortunately they only got her for a pasture ornament.
I'm at a loss for how to advise you with your gelding, it sounds like you've done all the right things. My sis' QH, Rio, has been similarly lame before, though, albeit not for as long. We once spent 2 weeks epsom-salt-soaking and applying liniment to one of his legs for an abscess. If your guy has an abscess in his foot, that may or may not show up in a radiograph (I'm not a vet, this is only what I've been told). Rio's abscess eventually worked out, and he's fine. He is accident prone, though, and the farrier frequently finds tiny "pockets" when he trims from healed abscesses that formed but never caused lameness. Rio's now on a hoof supplement.
Going by what you have ruled out, I would say look into the possibility of an abscess causing your horse's lameness, especially if your vet has already suspected an injury incurred in pasture play.