what do the color codes mean on the little boxes (bosses i assume) shown by the instances in the right hand panel; I see green, pink, yellow, and gray

I'm not sure which panel you're talking about

He means the raid difficulty colors.

Red, blue, yellow, green, etc.

I also think he might be color blind with the pink and grey?

That or monitor colors could be super off

or he could mean the colors on the main premade tab when doing regular bgs

What I know is...

Green: Normal mode

Red: Heroic mode

Yellow: Flex

Bllue? I have no clue