Got the routing working to a safe degree.

src/main/java/WayofTime/bloodmagic/block/BlockMasterRoutingNode.java

@@ -6,7 +6,7 @@ import net.minecraft.tileentity.TileEntity;
 import net.minecraft.world.World;
 import WayofTime.bloodmagic.BloodMagic;
 import WayofTime.bloodmagic.api.Constants;
-import WayofTime.bloodmagic.routing.TileMasterRoutingNode;
+import WayofTime.bloodmagic.tile.routing.TileMasterRoutingNode;
 
 public class BlockMasterRoutingNode extends BlockContainer
 {

src/main/java/WayofTime/bloodmagic/registry/ModBlocks.java

@@ -31,7 +31,6 @@ import WayofTime.bloodmagic.item.block.ItemBlockCrystal;
 import WayofTime.bloodmagic.item.block.ItemBlockPedestal;
 import WayofTime.bloodmagic.item.block.ItemBlockRitualController;
 import WayofTime.bloodmagic.item.block.ItemBlockRitualStone;
-import WayofTime.bloodmagic.routing.TileMasterRoutingNode;
 import WayofTime.bloodmagic.tile.TileAlchemyArray;
 import WayofTime.bloodmagic.tile.TileAltar;
 import WayofTime.bloodmagic.tile.TileImperfectRitualStone;
@@ -42,6 +41,7 @@ import WayofTime.bloodmagic.tile.TileSoulForge;
 import WayofTime.bloodmagic.tile.TileSpectralBlock;
 import WayofTime.bloodmagic.tile.TileTeleposer;
 import WayofTime.bloodmagic.tile.routing.TileInputRoutingNode;
+import WayofTime.bloodmagic.tile.routing.TileMasterRoutingNode;
 import WayofTime.bloodmagic.tile.routing.TileOutputRoutingNode;
 import WayofTime.bloodmagic.util.helper.InventoryRenderHelper;
 

src/main/java/WayofTime/bloodmagic/routing/TestItemFilter.java

@@ -182,9 +182,12 @@ public class TestItemFilter implements IItemFilter
 
         ItemStack testStack = inputStack.copy();
         testStack.stackSize = allowedAmount;
-        ItemStack remainderStack = Utils.insertStackIntoInventory(testStack, accessedInventory, accessedSide, allowedAmount);
+        ItemStack remainderStack = Utils.insertStackIntoInventory(testStack, accessedInventory, accessedSide);
+//        System.out.println("Remaining stack size: " + (remainderStack != null ? remainderStack.stackSize : 0) + ", allowed amount: " + allowedAmount);
 
-        int changeAmount = inputStack.stackSize - (remainderStack == null ? 0 : remainderStack.stackSize);
+        int changeAmount = allowedAmount - (remainderStack == null ? 0 : remainderStack.stackSize);
+        testStack = inputStack.copy();
+        testStack.stackSize -= changeAmount;
 
         for (ItemStack filterStack : requestList)
         {
@@ -198,7 +201,7 @@ public class TestItemFilter implements IItemFilter
             }
         }
 
-        return remainderStack;
+        return testStack;
     }
 
     /**
@@ -254,6 +257,8 @@ public class TestItemFilter implements IItemFilter
             ItemStack testStack = inputStack.copy();
             testStack.stackSize = allowedAmount;
             ItemStack remainderStack = outputFilter.transferStackThroughOutputFilter(testStack);
+            int changeAmount = allowedAmount - (remainderStack == null ? 0 : remainderStack.stackSize);
+//            System.out.println("Change amount: " + changeAmount);
 
             if (remainderStack != null && remainderStack.stackSize == allowedAmount)
             {
@@ -261,9 +266,9 @@ public class TestItemFilter implements IItemFilter
                 continue;
             }
 
-            accessedInventory.setInventorySlotContents(slot, remainderStack); //Sets the slot in the inventory
+            inputStack.stackSize -= changeAmount;
 
-            int changeAmount = inputStack.stackSize - (remainderStack == null ? 0 : remainderStack.stackSize);
+            accessedInventory.setInventorySlotContents(slot, inputStack.stackSize <= 0 ? null : inputStack); //Sets the slot in the inventory
 
             for (ItemStack filterStack : requestList)
             {

src/main/java/WayofTime/bloodmagic/tile/routing/TileFilteredRoutingNode.java

@@ -26,6 +26,12 @@ public class TileFilteredRoutingNode extends TileRoutingNode implements ISidedIn
         }
     }
 
+    @Override
+    public boolean isInventoryConnectedToSide(EnumFacing side)
+    {
+        return true;
+    }
+
     @Override
     public void readFromNBT(NBTTagCompound tag)
     {

src/main/java/WayofTime/bloodmagic/tile/routing/TileMasterRoutingNode.java

@@ -1,4 +1,4 @@
-package WayofTime.bloodmagic.routing;
+package WayofTime.bloodmagic.tile.routing;
 
 import java.util.HashMap;
 import java.util.LinkedList;
@@ -14,6 +14,12 @@ import net.minecraft.util.EnumFacing;
 import net.minecraft.util.ITickable;
 import net.minecraft.world.World;
 import WayofTime.bloodmagic.api.Constants;
+import WayofTime.bloodmagic.routing.IInputItemRoutingNode;
+import WayofTime.bloodmagic.routing.IItemFilter;
+import WayofTime.bloodmagic.routing.IMasterRoutingNode;
+import WayofTime.bloodmagic.routing.IOutputItemRoutingNode;
+import WayofTime.bloodmagic.routing.IRoutingNode;
+import WayofTime.bloodmagic.routing.NodeHelper;
 
 public class TileMasterRoutingNode extends TileEntity implements IMasterRoutingNode, ITickable
 {
@@ -46,6 +52,7 @@ public class TileMasterRoutingNode extends TileEntity implements IMasterRoutingN
                 {
                     if (!outputNode.isInventoryConnectedToSide(facing) || !outputNode.isOutput(facing))
                     {
+                        System.out.println("Hello");
                         continue;
                     }
 

src/main/java/WayofTime/bloodmagic/util/GhostItemHelper.java

@@ -55,6 +55,10 @@ public class GhostItemHelper
         NBTTagCompound tag = newStack.getTagCompound();
         int amount = getItemGhostAmount(ghostStack);
         tag.removeTag(Constants.NBT.GHOST_STACK_SIZE);
+        if (tag.hasNoTags())
+        {
+            newStack.setTagCompound(null);
+        }
         newStack.stackSize = amount;
 
         return newStack;