End of boil won't affect flavor, just aroma. (Well, it might affect flavor a little as there's still plenty of heat.)
You're not really supposed to boil hopped extract kits. If you wanted some flavor hops, you could probably boil a little of the extract for 10-15 minutes with some hops, then add some more when you kill the heat and add the rest of the extract.
EKGs and Fuggles would work good for either position, more so than Challenger (although this may be a matter of taste).