Hi !
First I'd like to say this is a great idea you got there.
Now the problem : it seems you can't go through the early-game with the Angel Smelting Patch installed. (I precise I run full Bob's + full Angel) The reason for this is the fact that the omnite extractor only allows at first to extract iron and copper out of it. It might be fine without the patch, but with it you can't smelt iron or ore in a stone furnace in order to force the player to go down the smelting path, which means you can't actually craft anything.
My suggestion is, if the patch is installed, to allow extraction of Saphirite or Stiratite the same way you can extract iron or copper, keeping the crappy efficiency of doing it to force the player to research better methods of extraction (maybe change crafting time too ?)