I found this to handle the changes in block and items ids so you can convert a world of 1.06 to a new world of 1.18, the only issue I have so far is that Balkons weapon names and the power gauntlet changed in the item code but other than changing that to match everything works.
Used this http://www.minecraftforum.net/topic/1636125-midas-patch-maker-midas-gold-convert-your-world-world-block-item-id-converter-for-mods/ to make the block conversion.
It seems that most Applied Energistics changed ids so take care of that. Suggesting that you place everything on normal chests before the upgrade.