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I would recommend WorldEdit.
It has the command:
//replace [current_block_ID] [new_block_ID]
Edit:
Although there is no way of formatting a whole world from a block, you would have to select a smaller area and replace.
Another good program is McEdit.
Tried WorldEdit, but it would not replace itemducts with item id 20256:something. Dont remember the exact itemid now, but it said "20256" isn't recognized.
You could also use WE's "//set [block]" command it sets everyhting in the selection to air, etc regardless of if replacing modded blocks or not. I've used it to get rid of some of those Railcraft invisible blocks blocking a couple things (before I turned them off). Since it does only work with vanilla blocks you would still need to go into creative or have the ducts on hand to replace the glitched out ones with.