Balrog and servants of Sauron

[the phantom]

they'd be pretty self suffient, with their own chieftans etc. they would have thought themselves independent

Very true, Osse. Azog (the Orc King) certainly sounded independent in his message to the dwarves after branding his name on Thror-

But if his family wish to know who is now king here, the name is written on his face. I wrote it! I killed him! I am the master!

And also you said-

Sauron didnt say; "You orcs... go retake moria... you orcs go plague the passes."
They were already there

This was my conclusion as well. Note that the entry for 2480 makes the statement that the orcs "begin to make secret strongholds" in a seperate sentence than (and before) it says "Sauron begins to people Moria". The two could be entirely unrelated except by date. Maybe the orcs just happenned to be expanding at the same time that Sauron is messing with Moria. Moria and the passes are not the same exact thing after all though they are in the same general geographic region.