I have a thermally efficient 1914 bungalow in western Canada (read cold winters). My high heat loss occurs through my original picture and double hung windows. As I have a fairly high efficient gas furnace that has a fresh air intake and an electronic air filter coupled with a low speed constant circular fan, I have been able to seal all but a few windows from the inside. I do like the look of the original windows with storms but thermal efficiency demands that something be done. I am contemplating the purchase of custom-made double pane sealed units so as to install them between the window and the storm with stops and sealant.

My questions is can anyone tell me if I shall get the same thermal efficiency as the installation of a new wooden frame window with a pre-hung double pane sealed unit? Secondly, if the thermal efficiency will be compromised, to what extent and why?  

If I understood your post correctly, you are considering placing a dual pane IG unit between your exisiting window and storm and you are wondering if that will give you equal or better energy performance versus replacing your original windows? 

I have never heard anyone suggest that before.  It is a very interesting idea, but I would be a bit concerned that every window that has that "system" is now a fixed window and unless you pull the IG out, you won't be able to use the windows for ventilation.

Are you considering LowE coatings or gas infill in the IG units?

If not, then you will end up with a quad pane hybrid (part operating and part fixed), that won't have quite the same performance as a designed quad pane IG (and there aren't many of those around).

Adding LowE and gas fill to the IG will increase performance versus a non-LowE / non-gas infill window over using clear glass. 

Four lites of clear glass will have a U-factor (US version) of about .25.  This is a good number, especially when you don't want to change the windows for aesthetic reasons, but there are triple windows on the market that can reach .15 range or so, but they can be very expensive, adding an IG with LowE and gas might get you in that same range.