This is my first time hatching, but from what I've read on other posts, there are a few tough things about staggered hatches:
*the hum needs to be higher on the last three days, so the "younger" eggs will have extra humidity when they don't need it
*you have to be careful to mark the eggs so you know which to turn and which to leave alone, and when... (if you have an auto turner you'll probably have to switch to manual because the hatching chicks can get hurt in the auto turner)
Haven't read anything about bacteria. BYCers have successfully hatched staggered hatches, though! and yours aren't terribly different. I just set some eggs 1 day apart, so I feel your pain -- darn USPS... my eggs from VA arrived 2 days before my eggs from TX, even though TX is way closer to CA!