1) Was there any particular naming scheme set to the Angels. That is, 
did the Dead Sea Scrolls tell what their names were, or were they 
assigned by NERV and/or SEELE accordingly?

Up for grabs with regards to actual cannon sources. It could go either
way, depending on what you need for your fic.

2) Anybody know of anyplace where potential names for other Angels can 
be found, keeping with the "spirit" of the original names? In 
particular, I'm looking for a name that could be applied to a female 
Angel. I vaguely recall seeing something like this a long time ago, but 
damned if I can find it now.

Try any book on Kabbalah. Or the bible/Torah. Also the Koran.

Jerico