one problem that you could run into is the spacing within the frame. I think the spacing on the rear track fork ends is 120mm. moutan hubs are 135mm wich gives the wheel less dish and thus stronger(not a worry on a fixed gear, no dish!). if you want to re lace a 120mm hub on a 26 wheel this would change the ride/handling. beacuse of the fork rake, the stability of the frame is dictated by the size of the wheel. if you shrink the size of the wheel you decrease the effective fork rake and make your bike less stable. This bike was made for 700 road wheels. just go with it.
what is your standover height? that should be your frame size.