Deepest appologies, but I am going to hop on a soap box for a minute...
As someone who deals with chemicals on a daily basis I'd like to suggest the use of Phosphoric acid instead of Muratic acid.
First, I'll to point out that most commercial rust removers ("Naval Jelly" and CLR for example) use Phosphoric Acid as their active ingredient. I'm guessing some chemist out there figured out that Phosphoric Acid is the best to use, so who am I to argue?
I'm guessing plenty of us here have used Navel Jelly, so you guys will know that it's thick and clings easily to odd shapes with just a little burshing. Great stuff, IMO.
For a bicycle chain, I would suggest checking out the heavy duty bathroom tile cleaners available at the local hardware store. Just check the ingredients to verify the content of Phosphoric Acid. Sometimes its offered in a concentrated form and this stuff is very aggressive! Good stuff, use with care like you would Muratic Acid. Side note: I moved into an apartment that needed additional cleaning so I used this stuff without diluting as directed, and I let it sit overnight. It took off the scale and rust.... as well as etching the chrome fixtures right down to the brass. doh!
The added benifit is that Phosphoric acid is better for the environment. It's used as a component of fertilizers and (gasp!) is an ingredient in Coca Cola and other soft drinks!
Muratic Acid (aka Hydrochloric Acid) is a fairly nasty acid that is typically used in industrial applications and swimming pools. I've responded to several fires that resulted from the accidental mixing of Muratic Acid and oils (an apartment complex and a grociery store were the largest) and I have never responded to a fire from Phosphoric acid and anything.
Now I'll climb off my soap box and get a beer....
Edit: for your additional entertainment
http://en.wikipedia.org/wiki/Phosphoric_acid