The question as posed is to broad for a simple succinct answer. It broad terms it is "best" to isolate cause, effect and consequential quantum as discretely as possible. The spectrum of requests for equitable adjustment claims runs from highly discrete individual claims to comprehensive global time and cost claims. Discerning and defining the scope of as many discrete elements as possible and associated quantum allows cost to be isolated and  grouped by responsibility. The calculated value of these discrete elements are then deducted from the total cost overrun generating what is typically referred to as a "modified total cost claim" in which EOT cost can be isolated. 

The AACEI forensic white paper on forensic schedule analysis at http://www.aacei.org/resources/ppg/#PPG20 provides excellent guidelines as to how to review and analyze an as-built schedule relative to the project as-planned baseline. Due to the lack of common definition of terms and acronyms, this paper concentrates on process and methodology rather than terminology.  This is because the fact that while the forensic construction industry strives to establish commonality, there remain major differences between regions and nationalities in how various common verbiage and terms are defined.

A comprehensive searchable data base including interviews of key personnel coupled with as in depth knowledge of the components of the project record are critical to determining and proving cause, effect and quantum.While there are many means of compiling, filtering and grouping schedule and cost data, you can not make up what is not there.  A large part of the answer to "What is the best method to calculate EOT costs when the EOT has been cause by a number of variations initiated by the owners?" will be ultimately be determined by the information available to the analyst. In other words the first "best"method is to insure that comprehensive job cost records are maintained in sufficient detail to make discrete cost calculation possible. 

From my experience, the first two steps in any comprehensive schedule analysis should be to validate the baseline as-planned schedule and develop a comprehensive as-built schedule to completion. A complete modeling of the as-built schedule should include fragnets which represent events and non-events which impacted job progress but were not contemplated
nor modeled within the baseline schedule or its updates. This includes identifying and isolating interim critical delay(s) and mitigation(s). The calculation of EOT costs presupposes the  knowledge and ability to discern between direct cost and consequential time impacted "indirect" EOT costs. Keep in mind that while many costs include a time element, the calculation of costs overruns due to loss of efficiency, disruption, prolongation, changed scope, reduced productivity, forced (constructive) acceleration and similar issues may or may not involve an EOT.