I used to do quite a few bottle ships as a kid. But I'd use rubber thread instead of real sewing thread so I wouldn't have to construct the ship to accommodate the complex rigging necessary to pull up the masts and sails. The rubber thread would do the job by itself once the ship was in the bottle.
That was good fun then, but it goes without saying that these ships weren't made to last... So I have always wanted to do a bottle ship by the book. – Well, here it is, documented and all. Have fun.
Step 1: The secret behind the bottle ship
When I saw my first bottle ship as a kid, I was puzzled how it got into the bottle. Well now I know. You have to construct the ship in a way that allows the masts and booms to collapse. This way, the ship can be made small enough to enter the bottle through the bottleneck. Furthermore the rigging has to be made so you will be able to erect the masts again, once the ship is inside the bottle. The trick here is that the rigging to the left and right of the masts must be places a little behind the masts. Otherwise the masts won't be able to collapse and will not be kept in the right angle once they get erected into the upright position.
Other than you think, the sails have to be glued to the masts and not the booms to do the collapsing trick.
Fixing the treads is done with a tiny drop of wood glue.
Check out the principle drawings and you will understand.