Having read through (not in minute detail!) I think this is interesting, valuable work. I look forward to reading the finished piece.
One thing I think you should consider is clearly stating that these costs to publishers assume that all contributions by researchers are free (editorial and peer review contributions). If you did say this, I missed it :)
Some publishers do provide an honorarium or some sort of payment, more to editors than reviewers of course. This would be an interesting separate piece of work to establish how common this is and what average rates were. And of course it would also be interesting to know an estimated cost to the public purse of labour given to publishers for free by researchers.
Anyway, in your preprint, as I first read the abstract I was looking to for clarification of whether 'publishing costs' included peer review/editorial work or not. You say the study will calculate: "the costs associated with publishing primary research articles, from submission, through peer-review, to publication, indexing and archiving."
So you mention peer review here but you mean the mediation and management of the peer review process by publishers, not the cost of the labour involved by the people actually conducting that review (and editing).