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This particular ArrayIndexOutOfBoundsException is caused by calling the ItemAxe(ToolMaterial) constructor with a non-Vanilla ToolMaterial as it tries to look up the attack speed and damage using the ToolMaterial's ordinal as an array index. These arrays only have as many entries as their are Vanilla ToolMaterials, so any modded ToolMaterial's ordinal causes an ArrayIndexOutOfBoundsException. The solution is to use the ItemAxe(ToolMaterial, float, float) constructor and specify the attack damage and speed yourself.

Or you can copy and paste the files on your computer and declare it a new repository.

That is correct. Mod loading order only determines the order in which mods are passed the FML lifecycle events. If mod A requires mod B and mod B requires mod C then the loading order would be the following: Pre-Init: C, B, A -> Init: C, B, A -> Post-Init: C, B, A