Re: Capacity of Front Axle - My owner's manual says it holds 1.7 liters = 3.5 pints = about 1.8 quarts. So you actually got most of it out, and what you didn't get out will mix with the new stuff you put in. I wouldn't be worried about it.
Re: How long can I go before changing fluids again?
Engine oil - this is quite controversial, but you should be able to go longer intervals with syn oil. The best method is to have a used oil analysis done, this will tell you when the oil is no longer protecting the engine. I choose to just change it every 6k or so, this is very conservative with syn oil.
Front, Rear Axle - Gear lube and t-case lube doesn't get contaminated like engine oil does. With Syn gear lube, 100k is a reasonable interval. Again, the best way to tell is an oil analysis.
Trans - Ford recommends 60k for 'normal' service, 51k for 'severe' service for the 5R55E. In light of the problems that others have had with Exploder trannys, I'm going to use a 50k change interval with an external filter added to gather the extra bits floating around.
Transfer case - Ford recommends 60k for 'normal' service, 30k for 'severe' service. I will probably change at 50k when I do the tranny the next time.