Shipping to multiple locations for a single customer

I am hoping someone out there has a similar situation to ours and can
give us some advice. We have a customer that is a major retailer
with locations all around the country and frequently they do a
rollout of a product to some/all of their stores, and they have
changed the way they place these orders with us. They used to give us
one PO then give us a list of stores (up to 1600)and what items the
stores needed shipped. We never really found a good way to deal with
this situation in Epicor so we just created a single order in Epicor,
then creating and printing packing slips in our old ERP system
because we had a customization specifically for this that would
import the store lists and create the proper packing slips grouped by
ship date (since stores could be 1-4 transit days from us but they
all need them on the same day).
Now the customer has changed how they do things and we now receive a
unique PO for each store, and create a separate order for each store.
We have a service connect workflow we can use to get the orders in
the system, but we were wondering what the best way to create and
print the packing slips would be, without someone having to manually
go through and create a shipment with each order number. So far we
are planning on using service connect for this also, but we are
unsure how to select all the orders that belong together (i.e. have
the same ship date, but not orders that have the same ship date ).

To sum it up we need to figure out how group the by line item and
ship date and print all the packing lists and ship them.

Also we were wondering what other people do to automatically
calculate transit days, so that the ship date is different than the
need by date. Until now we were manually entering orders and changing
it ourselves, but this would become time consuming with 1000+ orders.

Sorry if that's alot of information, but we're hoping that someone
has a similar situation and could give us an example of how they do
it.

Thanks,
Brad