What was the difference between a 'special order' and lets say a 'regular' order, what made it special?
I'm sure that the difference then is the same as now: a "regular order" car is one made by order from a dealer; today, generally, few cars are made without an order in hand. I know Ford, at least, does not manufacture anything to inventory, there is a dealer order for every car manufactured. The dealers order what is either recommended for their inventory, or what they think will sell. A "special order" is one ordered for a specific customer to his/her specifications, and as John indicates, you have to be willing to wait for it. Not all dealers will take a special order, particularly if there is plenty of inventory around. Further, there are some other limitations to a "special order"; late in the model year production, for example, the production is all "queued up" for existing orders prior to M.Y. changeover; therefore they might not be able to accommodate your special order. Or, they might be producing certain colors only at certain times, or certain options may have been deleted mid-way through the model year, or otherwise unavailable. If one wants a "special order" it is best to start early in the model year cycle, and work with a cooperative salesman/dealer.
Some former "special orders" are probably not available. There used to be a few buyers in Alaska and Vermont who would want cars w/o air conditioning. I think that's hard to delete these days; its generally been made standard and also is an integral part of the "climate control" serving a purpose in defrosting.