That's kind of strange. I ask for clarification during peoples stories all the time. I'm not even apologetic, unless they were clearly midflow and talking quickly, in which case I'll make the question brief, and then encourage them to go on with the story once they've answered. When people do it to me, I take it as a sign they were actually trying to listen and process what I was telling them.

In a general sense, I'm not sure how to manage disagreements like that... I suspect it involves communication and talking about one's sodding feelings, because these kind of things ALWAYS involve that. I guess explain why you do it, and make it clear that you ARE listening, and that the questions are just so you can absorb the story better, and that his reaction to it is hurtful. But you probably do that anyway. It might just be an insoluble problem

The other big issue is that I grew up with a huge, loud family, where (at least in casual conversation) if you wanted to say something you had to jump on any chance to do so.

I catch myself interrupting people all the time. I don't mean to do it, but I have trouble sensing when to throw in my question or comment and then my brain obsesses over what I want to say and I have trouble continuing to focus on the conversation. I always feel bad after I interrupt someone, I'm just not always conscious of it until I've already annoyed them.

I generally do this too when someone's telling me a story, or relating something - usually its a matter of clarification, or I rephrase it in my mind, then vocalize that to make sure what I'm thinking of is correct.

To me, I'm usually more than alright on that sort of thing - talk's typically a two-way street, and asking for clarification on something usually expresses to me that you're both listening and interested.  As long as you don't end up completely disrupting the flow of the conversation, or all out derailing it against my will, then hey, talk is awesome.

Basically Johnny and I think similarly on this one.

In my experience, if someone *really* gets irritated at a little interruption like that, then it really puts me off.  At that point, the person telling the story isn't telling it to me.  He's telling it AT me.  And that's not cool.  A conversation isn't a stage, nor is it a one-man show.

I tend to avoid people like that.

Personally, the situation seems a little volatile.  A conversation's meant to be a give-and-take.  Assuming the interruptions aren't overly obtuse, completely disruptive, or a sign of inattentiveness, then from what you've told me, it sounds like he's more concerned about the "give" than the "take".  He expects you to sit quietly and let him perform before asking for input on his terms. 
I'd say talk to him about it - you amongst others here have always been the biggest proponents of clear, respectful, two-way communication, and it may be worth it to try to establish that. 
Beyond that, I won't be much help here, unfortunately.