All species are transitional

Other types of isolation include behavioral isolation, where potential mates don't recognize each other's behavior as signals for mating; mechanical isolation, where organisms attempt to mate but are physically unable to unite sperm and egg (perhaps the penis is too large, or the sperm cannot survive the environment of the vagina); or even seasonal/temporal isolation, where potential mates simply do not become ready to mate in synchronicity (boy, who hasn't had that problem?)Any of these situations, which are not themselves neccesarily genetic in nature, can interrupt gene flow between two populations, and lead eventually to the sorts of genetic changes that result in complete genetic incompatibility.

I don't know. Any number of things, I suppose, ranging from the biochemical and genetic to the social and communal. Offhand I don't know of any relevant examples, I'm sorry.

Huh? Transitioning?How does that make any sense? The fossil record is a record of dead organisms. Transition from one form to another is something that happens to populations, not to individuals.Therefore no one fossil can "transition." That's not an expectation coherent with sense. Quick, driver - follow those goalposts!

I think you're going to find it's a lot harder to draw the line than you'd like it to be.By analogy - one drop of water is not rain. Ten drops of water, not rain. An inch in an hour - that's definately rain. So when did it start raining? There's no clear line to be drawn; you could say "after 1000 drops" but it's not really raining any less at 999 drops, or any more at 1001 drops.You can tell when its raining. You can tell when its not raining. But any line you draw between "raining" and "not raining" is going to be arbitrary, because, contrary to the black-and-white nature of the way we've constructed language to describe the weather, there's a continumm between raining and not-raining.Another way to look at it is probabilistically. At "not-raining", there's a 0% chance that you would be correct to say it was raining. At "raining", there's a 100% chance that you would be correct to say so. Somewhere in between there was a 50% chance that it was raining at that point in time, but there's no way to know 100% if it was raining or not. At that point, your confidence in your statement that it is raining is only 50%.So too with species. Sorry if the analogy was tortuous.

I don't understand how you could. It's self-evident to me that gene flow exists between a parent and its offspring; thus, no reproductive isolation.

The moment that they are "totally isolated" is completely arbitrary. That's what's arbitrary about it - it's arbitrariness.