I've only skimmed through the last couple of pages, and haven't fully got on board with how this topic evolved here yet. Going cold at it though, my feeling is that identity, in the sense of individuated objects, is an emergent property and isn't a fundamental one. I think it's best to think of nature hosting distinct objects only relative to particular perspectives. For example, in the case of objects humans are familiar with, they are only distinct when seen on a large enough scale - which is how we normally see and think. If you look at subatomic levels though, everything we are familiar with is made up of quarks, electrons, and the bosons that bind them or repel them - it's impossible to lable and distinguish between these particles, and they aren't even well defined things of the sort we are used to because they are in a sense fundamentally indeterminate, yet everything we know of is made of them.
Another perspective is that of time. We almost always think of an object's distinctness as it is at a frozen point in time, but this is not the reality if you look at things longitudinally throughout extended time. Your example of the boat is a good one - and even more spectacularly, this is true of people too, because all our atoms and cells are replaced over and over during our lifetimes. I'm not made up of any of the same stuff as 10 years ago, but it goes deeper than that because I'm not the same person as I was when I was 8 years old. Extrapolate across the whole of time, and there is a tree of becoming that binds everything together in a vast network that started in the big bang, and where everything merges together into a single trunk at the beginning, and all apparently distinct objects are actually branches and twigs on this huge tree.
So what is it that gives identity? It seems to be something a little ghostly - a pattern, a configuration, and the relationship of this with other patterns and configurations. Mostly it's like this:
The cloud remains a coherent shape yet it's constantly being reformed - its substance is not the same from one minute to the next. Persistent eddies and waves in a stream of water are the same, and so are people on a longer timescale, and so are rocks and mountains on an even longer timescale.
So to a great extent, I think identity is in the eye, and at the convenience (or inconvenience lol), of a beholder, and their particular needs and purposes, and is actually more to do with software than hardware. Of course the danger then is that we get too clever, and start to think in terms of software templates, heirarchies of identity (humanity v John K for example), and idealised generalisations of identities, and then we may run headlong into Plato, but that's another story lol.