While I have the top end off the motor........
Should I clean all the black off the pistons and valves?
And the oil sheen inside the intake and plenum, should it be cleaned off?

Any light bulbs pop up for any other lil thing I should do before reassembly?

 

I would worry more about the valves then the pistons. Why do you have the top of the motor apart? Are you doing the head gaskets? If you are then I would recommend taking the heads to a machine shop for a valve job and resurface. They should clean your heads and valves for you. If you take your heads in to get a valve job be sure to have the blue valve stem seals from the head gasket kit with you because the shop probably won't have them in house and will have to order just as you would.

Before and after the machine shop

 

I just realized that you were the one with the wrench in the motor.
What did you decide to do with the truck? If you are going to put it back together and just sell it then please disregard what I said about the machine shop and don't bother cleaning anything. If you are going to keep the truck then now would be the best time to do the head gaskets and clean stuff.

 

wrench in the motor? sounds like something i would do.