Hi...
Our company has entries from 2009 and we are using nav5.0, from past 1 year we are unable to run batch job "Item cost Adjustment" for some Raw material items.. due to this we are facing the problem of cost for FG items also.. it was taking long time but still unable to complete..
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poor performance in NAV ACIE seems a never ending story and you can find dozen of articles.
I had similar issue and my advise are:
1 . check if you have patched with latest MS hotfix objects C5895, T5802, T339
2. be sure that SQL statistics/indexes are updated for Value and Item LedgeEntry
3. create e pre report that call R795 doing a commit after each item has been processed
Good luck