First thing first, you shouldn't ever have to run your seat all the way back in the rails, ever. I have a feeling even a set-back post might not help you enormously, if it's that far back. What size did you get, if they didn't have any 53s?
Strange you mention this fit issue, as I've had the very same issue with a LeMond of my own, '02 as well, a Tourmalet, so really just about the same frame as you. I think the shop I bought from dumped me into a too-small size (a 53), and I went with it at the time, being a long time lay-off from cycling, and not knowing any better. And like you, I felt good with my stem length, in fact feeling a little twitchy and lacking control with a longer stem. My seat is in the "ideal" position in the clamps, but I use a non-set-back post. Of course, looking at it now, I think I mostly started noticing the fit issue when I started getting into better shape, but back to the topic at hand, I also feel a little cramped on it now and much prefer to ride my new bike, which at a 54 is basically, supposedly, the same size, just measured c-t rather than c-c. LeMond touts the long top tube thing as unique, but I'm not so sure it's any longer than many other bikes.
Edit: Measuring both of my bikes' "effective" top tubes (one has a sloping top tube) just now, the Specialized's is nearly 3/4 of an inch longer at a comparitive point. I have a 90mm stem on each, and a post with only marginal set-back on the Specialized, but I feel great on the bike. I have about an inch and a half of length difference from center of seat clamp to center of handlebar clamp on the two bikes, the Specialized the longer, which could be explained by geometry. LeMond pushing a load of hooey on us about comparitive top tube length, perhaps? Ahh, marketing ploys. Gotta love 'em. I have a sneaking suspicion you're riding the wrong size for you.