Man Trek sounds like a PITA to work with! I'll second the Jamis recommendation, they are nice bikes. I'd also like to add a Fuji rec. Okay, okay, I'm biased since I ride one, but honestly they make nice road bikes and in a stellar variety of sizes. I agree with the fun apparel crowd and also, make sure you have some cold weather stuff! It bites walking into a store that only has one style of tights for instance.

I think having a women's only store is a good idea, and I would definately frequent one. It would be far less intimidating for beginners and refreshing for the rest of us. I bet ladies would be willing to travel long distances to visit such a store too. Another men's item to stock would be shoes for us wide webfooters out here. ;-)