hmmm, i think the sail could be applied to the large version of the boat with no issues.
the keel seems to be designed to be an attachable object, given that the keel of the boat is the largest part of the frame on the bottom, and the part to which all the other parts are attached and built upon. to replace a keel, one would literally have to disassemble the entire boat... which i do not get the impression is the intent of the item.
so i would conclude that the keel should have to be built into the item from the get-go, or it should be attachable. magic items frequently can size themselves, so if the keel can attach, perhaps it should be able to gain the shrinking abilities. perhaps quietly take the cost of the extra ability (from the dmg / mic for adding abilities to an item) out of the treasure they find for the next few portions of the adventure so that they can get the cool ability and fun adventuring without having to foot the cost all at once or upfront.
you could even turn it into a plot hook, wizard will do the work in exchange for a few "minor" tasks that require the use of just such a craft....
those are my mechanical thoughts.
as far as story or plot goes?
i say banzai!!!
go for it, that is a great idea. make it work somehow. =D do remember the stronghold builders guidebook for ideas on turning the boat into a flying fortress or for souping up the boat in general.