1. How long after hatching do neonates shed?
Mine have averaged about 7-10 days after hatching. When mine hatch, they are well on their way into a shed cycle.
2. How long must I leave them in the hatching container for them all to shed?
The whole time. 
3. I do reach in and remove the shells and other debris, to prevent the possibility of anything bad growing, right?
Ya, Rich even mentioned doing so in that thread.
What I did last year was take them out of the egg box and put them into another small setup with a water dish, plenty of hides, and wet moss as a substrate... just like the eggbox. It just seems "cleaner" for them. 
I think the idea he was trying to get across was to not go crazy with bothering them while they are pipping. (I think we've all been guilty of that at some point.) Once they've hatched, it's also important to remember that they are already well on their way into a shed cycle. Some will be not in the mood to be handled or bothered, and it's easier to damage them while they are in that phase.
Plus, that first shed is a very dramatic change, and at that point you'll get a much better look at their colors anyway.
And shepherds we shall be, for thee my lord for thee. Power hath decended forth from thy hand so our feet may swiftly carry out thy command. And we shall flow a river forth to thee and teeming with souls shall it ever be. In nomine Patris, et Filii, et Spiritus Sancti." - The Boondock Saints
In pectorum quid pro qum.
In pecunium sic transit gloria.
I didn't know Gloria was sick!
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Useful stuff on the Serpentine Widgets website:
Morph Library
Genetics and Inheritance Tutorial
Snake Measuring Program
Cornsnake Glossary
