1. Can we re-use this hive? or might it be contaminated in some way?
If there was no evidence of AFB use away. Better to reuse it, the drawn comb will give the new tenants a head start.
2. Should we try to reuse the empty comb that is left? (notice how dark and black it looks?)
Yes, by all means. Dark comb means brood comb unless the comb is 5 years old or older I'd go ahead and use it.
3. There was still some capped honey frames, can we reuse those?
Yes, to that too. It will reduce or do away with having to feed a package.
4. If we reuse the frames, what's the best way to clean them up and remove the dead bees?
Let the bees do it, they are very good at it. they will remove dead bees and everything that needs cleaning up unless you have excessive wax moth damage, then cut out the comb and put in new foundation.
5. Should we start with some new frames, all new frames or what combination?
The frames you have will be sufficient. If you want to build them up fast take 1 or 2 frames out of each box, replacing them with new frames and put them into a 3rd box with mixed draen and undrawn frames. You should be a strong 3 box hive my mid-June even if you get your package in late April
6. There are still a few bees still flying in and out, should we clear them out in some way?
Do they live there, if so your hive is still alive--nurse with syrup and pollen patties. If they are robber bees remove any remaining honey frames for use with your package or it will be gone.
7. Should we move the hive, disassemble it and "air-it-out"?
Moving it is not necessary unless you have a better spot for your bee yard. Just clean it up (remove bottom board and shake it out and replace it) and leave it alone. A swarm might decide to establish residence.
8. What else can we do to assure success of the new colony?
Study Michael Bush's web site and the info on this forum.