I fitted new rear toe links last weekend due to the bushes
being shot and scrubbing my NSR tyre on the outer edge.

I had 4 wheel Lazer alignment done today.

My question is what ride height should the car be in while
the alignment is being carried out??

I'm not happy with the result of the alignment.
He basically managed to adjust the toe front and back but both NSF & NSR are both still out. He says there is no more adjustment left. Both OSF and OSR are pretty much spot on.

With the rear toe links being new why won't the NSR come into tolerance??

Alignment is at standard height ( best if you can set the suspension in tight tolerance mode in workshop tool like the GAP IID) Are the camber and castor within spec? Check all the bushes and joints for wear and play. If all good and the hub won’t adjust to within spec then you have to consider bent arms or other damage. 2012 TDV8 Vogue (L322)

Before

Click image to enlarge

Both rear rose bushes were replaced last year as well

Camber is all good it's just that rear toe on the NS that is still the issue

Mines the same but on the rear right. I suspect the replacement rear toe arm is a smidge longer.
I plan on welding some extra metal onto the cam adjusters when the weather improves to give it that final nudge back into line.

car should be put into "High Tolerance " to make those adjustments. 2012 Vogue 4.4 TDV8 - Current
2014 Navara V6 - Gone
2004 Vogue TD6 - Gone
Grand Cherokee - Gone
Discovery V8 (LPG) - Gone
Discovery TD5 - Gone

I think you mean 'tight tolerance' - useful but not essential and the standard procedure for alignment is to change the suspension height up and then down to settle it before measurement and adjustment. 2012 TDV8 Vogue (L322)