Thanks for the information Verb - the reason we track those other keywords separately from traffic is because I normally find their rank a good marker around the primary keywords but I understand what you're saying so there is more clarity in the focus.
I'll look for one of those tools and see if SEOprofiler works or similar. I've done the adwords method before but it's a bit laborious so I would prefer something automated if possible.
Thanks for the reassurance! It appears that yesterday evenings tracking in moz has updated and a lot of keywords have gone back up again so fingers crossed there was just a glitch / settling in phase!
Thanks