Initialize methods after loading classgroup too, I dont know if other things are broken elsewhere. Making the method graphs work makes many more frames. Might be worth processing methods one at a time and then doing the comparisons. And maybe elsewhere that doesn't need the graph will not include all frames, or something.

src/main/java/net/runelite/deob/ClassGroup.java

@@ -45,6 +45,12 @@ public class ClassGroup
 		return null;
 	}
 	
+	public void initialize()
+	{
+		buildClassGraph();
+		lookup();
+	}
+
 	public void buildClassGraph()
 	{
 		for (ClassFile c : classes)

src/main/java/net/runelite/deob/util/JarUtil.java

@@ -35,6 +35,8 @@ public class JarUtil
 			}
 		}
 		
+		group.initialize();
+		
 		return group;
 	}