Going back to the original query. Our MTO5 got a band 8b on direct matching. There are sufficient profiles that a JAQ should be unnecessary; have you compared your own job description against the generic healthcare scientist profiles or the "manager of a clinical / clinical technical service profiles? If you find a reasonable fit it is possible to suggest appropriate profiles to the matching panels.( i.e. staple them to your job description)
As far as JAQ's go just stick down everything they ask for, if your HR are following the correct procedure then you should have an informal interview/help session where some trained matchers will run through your completed JAQ with you and help you put in anything you may have forgotten.
Now back to the griping - Why should a manager be paid more than the staff they manage? It is increasingly common, where afc is being applied properly, to find that skilled staff are paid more than their unskilled managers - people management responsibility is worth a lot less than knowledge and experience.
All job comparison schemes have their flaws but are essential in the modern climate as they are the best defence against equal pay claims and AFC is one of the best such schemes around (and yes EVERYBODY thinks that is biased against their particular area [which it is

])