There are apartments above the shops downtown and they're EXXACTLY what you're looking for. I know a few people who live in them. And don't worry a 1 bedroom runs for less than $500. Most people just put signs in the windows. It's next to impossible to find something about them online.
This grocery store is in the same building as some lofts. They may be able to help:
Home
These people own the bed and breakfast above Delmonico Grll downtown. They may be able to help:
Phone: +1-605-716-3405
Fax: +1-605-341-4448
Cellular: +1-605-431-7383
I also found this article on the new lofts above the piano store on Saint Joseph Street:
Decorating a Loft Rapid City SD - Rapid City SD, loft decoration, Rapid City SD loft apartments, Rapid City SD loft decor, Rapid City SD loft design, Rapid City SD loft remodeling services (http://local.bobvila.com/Decorating_a_Loft_Rapid_City_SD-r1222409-Rapid_City_SD.html - broken link)