Basically shake out dead bees as good as you can, clean bottom board,
I wash with soapy water...on all hives in spring. Bees will clean up the rest,.. even take out dead bees stuck in their cells.

Will I need to restock with a colony or will bees come back. noticed some activity. also some honey left in the shallow. should I leave that. what about the wax and the dark cells in the super.

It looks like you have robbing going on when you see some bees go in
and out, theyr'e stealing the honey. You need a inspection to see what's going on inside. If so, close off the hive and get a new package. What is the dark ....are these bees? Perhaps mold, to some degree they can clean it up, I would scrape off most first.