Re: now explain this, hookahpros. . .
to answer the first portion... It happens all of the time on my brass musical instruments... when i wipe down the valves/slides before cleaning them it's a greenish color that it sounds like you're describing... Probably just the moisture reacting with the brass... nothing to worry about IMO...
the last bit: when i plug one end to clean the stem, i use my left hand middle finger to plug it, and use my other fingers/palm to steady the stem, and i use my right hand to pour the water in and use a cleaning brush.
Feels wicked uncomfortable... but you gotta do what ya gotta do, i guess.