We have a fairly new, very small shop in a nearby town and I've helped them figure out what to stock. Its tough as heck to have everything in stock though, even farily large shops don't stock every specialty grain there is.
That said, if the prices are too much over mail order then you will lose business, plain and simple. The new people started with some pretty high prices and turned off a lot of new customers right off the bat, and I think they're suffering for it. I would at least start on the low side and ramp up slowly, or run regular sales.
Something our LHBS does is to run regular pallet orders and offer a discount on those, it helps them defray their shipping costs, make a few bucks and not have to store so much stuff at the store. It gives club members (and anyone else) the opportunity to order exactly what they want. This is also how the next closest LHBS runs, and they vary which supplier they go through which gives me access to great variety of malts and products.
You might also find a source for corny kegs and offer them at decent prices. Equipping your customer base properly will make it easier for them to brew more beer.