What regulations cover development of the CoEI during technical manual development?
COEI is governed by AR 71-32, Force Development and Documentation - Consolidated Policies. A COEI belongs as part of a Class VII end item and normally has no separate identity outside of that end item. AR 71-32, para 6-23, states that a COEI could be a separate end item.
The final decision on any issues would be jointly determined between the PM and the MDA.
There is additional information located on the DAU Ask A Professor homepage. Specifically, https://dap.dau.mil/aap/pages/search.aspx?q=coei