Even if your local bike shop doesn't carry the bike you want, many will special order. Certainly LBS will order frames only, although that will be special order. If they can't or won't, you can call around to other independent bike shops and order from them. The difference is in the small, customer-oriented shop vs. the big corporation that doesn't know or care who you are.

Now that the season is underway and there's no usable bike, I wonder how much of a good deal it was?

I hope you get it worked out with them soon.