You are correct in your thinking however for ease of people popping in to review the ruling I will break it down how it works.
Dude A has sword of the spirit cast on him (either by himself or another blessed) because he has a melee weapon.
Noon Miracle 7: Choose a dude with a Melee Weapon. While they have that Weapon (this turn), they have +1 bullets, become a stud, and cannot be affected by opposing spells.
Dude B then casts Phantom Fingers on the weapon attached to Dude A
Noon/Shootout Hex 6, Boot: Choose a goods card attached to an opposing dude in this or an adjacent location. Boot it, and it loses all traits, abilities, and bullet bonuses. If it's Mystical or a Gadget, draw a card.
Because phantom fingers targets the goods and not the dude this is a legal target. The melee weapon gets booted, loses all traits (not keywords) abilities and bullet bonuses.
Dude A still retains the effects from sword of the spirit. Stud and +1 bullet bonus however loses the bonus from the melee weapon itself as it no longer provides its own bullet bonus due to phantom fingers.