Any question answered...

Was the shifter in highest gear when you set the cable up?

Can you pull the cable by hand to get the chain to move to the lowest gear? Or is the low limit set incorrectly?

And why does your brand new chain look so dirty?

Yes

Cant pull by hand as there is not enough inner left so using pliers; I'll do the low limit setting again

Its not new; this is the 6700 groupset I had on a bike that I am trying to shift over.

Following this video: Shimano Ultegra 6700 Installation & Adjustment Guide on Vimeo

Do I have to do both low and top adjustment of RD without installing the cable? According to shimano manual it says do top > install cable > do low. If this is not the case at which position should I install cable? Biggest sprocket + small chainring?