Post-acquisition equity review: harmonise pay structures first or analyse the two apart?

We are a veterinary services group in the UK, and in March we acquired a competitor, taking us from 3,200 to about 5,100 employees. The acquired business has no grades, pays vets and nurses on individually negotiated salaries, and has a noticeably different gender mix at clinical director level.

Our annual audit is due in January. If I analyse the combined population using our structure, most of the acquired staff are unmapped. If I analyse them separately, I have one clean result and one that I already know will look poor, and I am not sure what I would be committing us to by documenting it.

Harmonisation is planned over 18 months. Has anyone been through this, and what did you do in the interim year?