Program: 165736
Project: 165736
Buggy source:
public static void initCrafting(){
  GameRegistry.addRecipe(new ItemStack(modularStorageBlock),"String_Node_Str","String_Node_Str","String_Node_Str",'M',ModBlocks.machineFrame,'c',Blocks.CHEST,'r',Items.REDSTONE,'q',Items.QUARTZ);
  GameRegistry.addRecipe(new ItemStack(remoteStorageBlock),"String_Node_Str","String_Node_Str","String_Node_Str",'M',ModBlocks.machineFrame,'c',Blocks.CHEST,'e',Items.ENDER_PEARL,'q',Items.QUARTZ);
  GameRegistry.addRecipe(new ItemStack(storageTerminalBlock),"String_Node_Str","String_Node_Str","String_Node_Str",'M',ModBlocks.machineBase,'g',Blocks.GLASS,'e',Items.ENDER_PEARL,'p',Items.PAPER);
  GameRegistry.addRecipe(new ItemStack(levelEmitterBlock),"String_Node_Str","String_Node_Str","String_Node_Str",'M',ModBlocks.machineBase,'g',Blocks.GLASS,'e',Items.ENDER_PEARL,'p',Items.PAPER,'c',Items.COMPARATOR);
  GameRegistry.addRecipe(new ItemStack(oreDictTypeItem),"String_Node_Str","String_Node_Str","String_Node_Str",'u',Blocks.IRON_ORE,'p',Items.PAPER,'r',Items.REDSTONE,'i',Items.IRON_INGOT);
  GameRegistry.addRecipe(new ItemStack(genericTypeItem),"String_Node_Str","String_Node_Str","String_Node_Str",'p',Items.PAPER,'r',Items.REDSTONE,'i',Items.IRON_INGOT);
  GameRegistry.addRecipe(new ItemStack(storageFilterItem),"String_Node_Str","String_Node_Str","String_Node_Str",'h',Blocks.HOPPER,'p',Items.PAPER,'r',Items.REDSTONE,'i',Items.IRON_INGOT);
  GameRegistry.addRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_EMPTY),"String_Node_Str","String_Node_Str","String_Node_Str",'g',Items.GOLD_NUGGET,'e',Items.EMERALD,'r',Blocks.REDSTONE_BLOCK,'q',Blocks.QUARTZ_BLOCK);
  GameRegistry.addRecipe(new ContainerAndItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_EMPTY),new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER1),new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_FULL),null));
  GameRegistry.addRecipe(new ContainerAndItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_EMPTY),new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER2),new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_FULL),null));
  GameRegistry.addRecipe(new ContainerAndItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_EMPTY),new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER3),new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_FULL),null));
  GameRegistry.addRecipe(new ContainerAndItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_EMPTY),new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_REMOTE),new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_FULL),null));
  GameRegistry.addRecipe(new ContainerAndItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_EMPTY),new ItemStack(ScreenSetup.storageControlModuleItem,1),new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_SCANNER),i -> META_FOR_SCANNER));
  GameRegistry.addRecipe(new ContainerToItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_FULL),new ItemStack(storageModuleItem),null));
  GameRegistry.addRecipe(new ContainerToItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_SCANNER),new ItemStack(ScreenSetup.storageControlModuleItem),n -> 0));
  GameRegistry.addRecipe(new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER1),"String_Node_Str","String_Node_Str","String_Node_Str",'r',Items.REDSTONE,'i',Items.IRON_INGOT,'g',Items.GOLD_NUGGET,'c',Blocks.CHEST,'q',Items.QUARTZ);
  GameRegistry.addRecipe(new PreservingShapedRecipe(3,3,new ItemStack[]{null,new ItemStack(Blocks.CHEST),null,new ItemStack(Items.GOLD_INGOT),new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER1),new ItemStack(Items.GOLD_INGOT),new ItemStack(Items.QUARTZ),new ItemStack(Items.REDSTONE),new ItemStack(Items.QUARTZ)},new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER2),4));
  GameRegistry.addRecipe(new PreservingShapedRecipe(3,3,new ItemStack[]{null,new ItemStack(Blocks.CHEST),null,new ItemStack(Blocks.GOLD_BLOCK),new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER2),new ItemStack(Blocks.GOLD_BLOCK),new ItemStack(Blocks.QUARTZ_BLOCK),new ItemStack(Blocks.REDSTONE_BLOCK),new ItemStack(Blocks.QUARTZ_BLOCK)},new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER3),4));
  GameRegistry.addRecipe(new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_REMOTE),"String_Node_Str","String_Node_Str","String_Node_Str",'r',Items.REDSTONE,'i',Items.IRON_INGOT,'g',Items.GOLD_NUGGET,'c',Blocks.CHEST,'q',Items.QUARTZ,'e',Items.ENDER_PEARL);
}

Fixed version (ground truth):
public static void initCrafting(){
  GameRegistry.addRecipe(new ItemStack(modularStorageBlock),"String_Node_Str","String_Node_Str","String_Node_Str",'M',ModBlocks.machineFrame,'c',Blocks.CHEST,'r',Items.REDSTONE,'q',Items.QUARTZ);
  GameRegistry.addRecipe(new ItemStack(remoteStorageBlock),"String_Node_Str","String_Node_Str","String_Node_Str",'M',ModBlocks.machineFrame,'c',Blocks.CHEST,'e',Items.ENDER_PEARL,'q',Items.QUARTZ);
  GameRegistry.addRecipe(new ItemStack(storageTerminalBlock),"String_Node_Str","String_Node_Str","String_Node_Str",'M',ModBlocks.machineBase,'g',Blocks.GLASS,'e',Items.ENDER_PEARL,'p',Items.PAPER);
  GameRegistry.addRecipe(new ItemStack(levelEmitterBlock),"String_Node_Str","String_Node_Str","String_Node_Str",'M',ModBlocks.machineBase,'g',Blocks.GLASS,'e',Items.ENDER_PEARL,'p',Items.PAPER,'c',Items.COMPARATOR);
  GameRegistry.addRecipe(new ItemStack(oreDictTypeItem),"String_Node_Str","String_Node_Str","String_Node_Str",'u',Blocks.IRON_ORE,'p',Items.PAPER,'r',Items.REDSTONE,'i',Items.IRON_INGOT);
  GameRegistry.addRecipe(new ItemStack(genericTypeItem),"String_Node_Str","String_Node_Str","String_Node_Str",'p',Items.PAPER,'r',Items.REDSTONE,'i',Items.IRON_INGOT);
  GameRegistry.addRecipe(new ItemStack(storageFilterItem),"String_Node_Str","String_Node_Str","String_Node_Str",'h',Blocks.HOPPER,'p',Items.PAPER,'r',Items.REDSTONE,'i',Items.IRON_INGOT);
  GameRegistry.addRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_EMPTY),"String_Node_Str","String_Node_Str","String_Node_Str",'g',Items.GOLD_NUGGET,'e',Items.EMERALD,'r',Blocks.REDSTONE_BLOCK,'q',Blocks.QUARTZ_BLOCK);
  GameRegistry.addRecipe(new ContainerAndItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_EMPTY),new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER1),new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_FULL),null));
  GameRegistry.addRecipe(new ContainerAndItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_EMPTY),new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER2),new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_FULL),null));
  GameRegistry.addRecipe(new ContainerAndItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_EMPTY),new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER3),new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_FULL),null));
  GameRegistry.addRecipe(new ContainerAndItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_EMPTY),new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_REMOTE),new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_FULL),null));
  GameRegistry.addRecipe(new ContainerAndItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_EMPTY),new ItemStack(ScreenSetup.storageControlModuleItem,1),new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_SCANNER),i -> META_FOR_SCANNER));
  GameRegistry.addRecipe(new ContainerToItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_FULL),new ItemStack(storageModuleItem),null));
  GameRegistry.addRecipe(new ContainerToItemRecipe(new ItemStack(storageModuleTabletItem,1,StorageModuleTabletItem.DAMAGE_SCANNER),new ItemStack(ScreenSetup.storageControlModuleItem),n -> 0));
  GameRegistry.addRecipe(new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER1),"String_Node_Str","String_Node_Str","String_Node_Str",'r',Items.REDSTONE,'i',Items.IRON_INGOT,'g',Items.GOLD_NUGGET,'c',Blocks.CHEST,'q',Items.QUARTZ);
  GameRegistry.addRecipe(new PreservingShapedRecipe(3,3,new ItemStack[]{ItemStackTools.getEmptyStack(),new ItemStack(Blocks.CHEST),ItemStackTools.getEmptyStack(),new ItemStack(Items.GOLD_INGOT),new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER1),new ItemStack(Items.GOLD_INGOT),new ItemStack(Items.QUARTZ),new ItemStack(Items.REDSTONE),new ItemStack(Items.QUARTZ)},new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER2),4));
  GameRegistry.addRecipe(new PreservingShapedRecipe(3,3,new ItemStack[]{ItemStackTools.getEmptyStack(),new ItemStack(Blocks.CHEST),ItemStackTools.getEmptyStack(),new ItemStack(Blocks.GOLD_BLOCK),new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER2),new ItemStack(Blocks.GOLD_BLOCK),new ItemStack(Blocks.QUARTZ_BLOCK),new ItemStack(Blocks.REDSTONE_BLOCK),new ItemStack(Blocks.QUARTZ_BLOCK)},new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_TIER3),4));
  GameRegistry.addRecipe(new ItemStack(storageModuleItem,1,StorageModuleItem.STORAGE_REMOTE),"String_Node_Str","String_Node_Str","String_Node_Str",'r',Items.REDSTONE,'i',Items.IRON_INGOT,'g',Items.GOLD_NUGGET,'c',Blocks.CHEST,'q',Items.QUARTZ,'e',Items.ENDER_PEARL);
}