Cutting (or at least loosening) the Gordian knot
Virtaully every organisation I've worked for has at one point or another embarked upon the same excerise and when you really start trying to calculate that it can become impossibly difficult. It 's everso easy to keep unravelling the minuatae of every process, work instruction and interaction, for instance; how to you calculate and cross-charge the cost of an engineer's time wasted by a user-inflicted IT issue (such as installing unauthorised software) or by a user who's lied or withheld a crucial nugget of information required to diagnose the fault (c'mon, we've ALL done it!).
I did work for an emplyer who must've eventually worked it out as all of a sudden desktop computer equipment was charged to the budget of the department requesting it (inc. cost of replacements and third-party engineer visits), the same for software too. Departmental projects that required the services of tech support would have to budget for the cost of the bodies they'd need.
However even with a rough idea of the cost and some measures of mitigation so much in a more general sense comes out of the IT budget than really should. Our cost centre used to bear the brunt of the cost of servicing and maintaining infrastructure equipment bought using capex. The reason the equipment had been capexed was that it comprised the core systems everyone used so it shouldn't come from one budget!
While many of the examples I've used admittedly involve shifting wooden dollars around sometime the best method of prepresenting 'The True Cost of IT' s to position the department almost as if it's a contractor, calculating and billing each department for the services and equipment they use. Whatever your approach, first agree a upon a level of detail you won't exceed, one that's managable for you and your business