Wow, so many questions, where to start.
When a hive swarms, they split and leave nurse bees and a queen cell behind, they don't just all up and leave, that would be absconding. My bet is your hive died.
Comb darkens the more times brood is raised in it, that is normal.
When you say second hive, do you mean replace your dead hive, or is that in addition to another hive you have? I'll assume you mean replace.
Packages will get off to a much quicker start if they have drawn comb verse foundation. If you are certain your bees didn't die from foulbrood, I would install you package on the drawn comb. Place empty combs towards the center and combs with honey to the outside.