I am building a home that has "historic" windows specified. These windows are specific enough that I will have to build them myself and there is no way to have double pane glass. I am wondering about the thermal performance of interior storm windows. Can I make a window with an interior storm window as efficient as a standard double pane window? Are there any known issues with interior storm windows?

You mean that historic commission will not allow double pane windows or that you can't build them?
You can buy double pane insulated glass panels from most glass companies that could be installed in your handmade sashes.

There is not a historic commission. The windows will have leaded glass similar to a stained glass window. Part of the window will use rondels or spun glass. Kind of hard to double insulate that sort of thing. Exterior storm windows would ruin the outside.

Any way to use insulated panels, and then mount your 'historic' glass as the interior 'storm' panel?
This would keep the handmade sashes out of the weather, and significantly increase their life expectancy.

According to the heat loss calculations provided to us by our geothermal installer, storm windows are more efficient than new double-paned glass.  In addition, double paned glass had a very high failure rate and often needs to be replaced in 10-15 years.  In addition, keeping your original windows means there are less items filling up a landfill.

It is for these reasons that I think it is much better to restore original windows than replace. 

Make sure all holes are sealed and weather stripping is used in all possible areas.  Use internal storms as necessary.  We decided to keep and restore our historic, original steel casement windows and I we are very happy that we did.  If you love old homes, in the long run, you will be happy that you did too.