Ghost ships get really deadly if you have enough of them to play every turn. Otherwise, if you give the opponent lots of gaps, they can just use the ghost ship turns to put back their good cards, and then have a REALLY good turn the turn after.
You played ghost ships on turns 5, 7, 13, 19. Always with gaps, sometimes with large ones. Ghost ships ruined individual hands, but not much more.
For reference, I just pulled up the Simulator's default ghost ship strategy, and looked at how it played against BMU: it ended up playing GS on turns 7,9,11,13,14,15,16,18,19,20. THAT'S a ghost ship lock. Your opponent did something more like that, but all those villages didn't really do that much for him. There's no need to play more than 1 GS a turn, as long as you play one every turn.
More ghosts ships. And yeah, you passed up some chances to buy estates in the late-game, that could have won you the game.