Is it necessary to use an external utillity like Auto HotKey?
I was able to set up modifier keys using the default/stock game by editing the inputbindings.dat file in a text editor. . . It seems to me the game already supports this there just isn't a way to set it in the game itself (since pressing shift/etc sets the key to shift).
Here's an example from my inputbindings.dat:
KeyBinding:Ingame_UseAbility0|Alpha0|Keypad0|None|None|None|None|None|10
KeyBinding:Ingame_UseAbility11|Alpha1|None|LeftShift|None|None|None|None|10
Those 2 entries set up the '0' key to use "power 10" (default) and then 'LeftShift + 1' to cast "power 11". It works for me in game, it's just not extremely user friendly to edit.
This works really, really well. The reason I hadn't used it before was the mouse. If you look at "mouse abilities" in the file, Mouse0-6 are in the 6th section. If you change that field anywhere outside of "mouse abilities" the game removes them.
You made me try again though, so thank you thank you thank you!
I put Mouse0-4 in the second slot, primary keyboard key. That and unbound the "mouse abilities." This works perfectly! (well, a minor cosmetic issue of "Mouse Button 1" doesn't fit nicely as the overlay, but whatever! I tried it as "alternate" but then it doesn't work) Consider me totally happy!
KeyBinding:TakeScreenshot|F12|None|None|None|None|None|None|10
KeyBinding:MarkAllLocalMessagesAsNew|BackQuote|None|None|None|None|None|None|10
KeyBinding:PauseLocalChunk|Q|Pause|None|None|None|None|None|10
KeyBinding:Debug|F3|None|None|None|None|None|None|10
KeyBinding:DebugNetwork|F2|None|None|None|None|None|None|10
KeyBinding:DebugCollision|F4|None|None|None|None|None|None|10
KeyBinding:DebugGhostInvisible|F5|None|None|None|None|None|None|10
KeyBinding:DebugBaseTileLayerInfo|F6|None|None|None|None|None|None|10
KeyBinding:DebugCTLTileLayerInfo|F6|None|LeftControl|None|None|None|None|10
KeyBinding:DebugEntityAlignmentMode|F7|None|None|None|None|None|None|10
KeyBinding:Ingame_Left|S|LeftArrow|None|None|None|None|Left|10
KeyBinding:Ingame_Right|F|RightArrow|None|None|None|None|Right|10
KeyBinding:Ingame_Down|D|DownArrow|None|None|None|None|Down|10
KeyBinding:Ingame_Up|E|UpArrow|None|None|None|None|Up|10
KeyBinding:Ingame_Jump|Space|None|None|None|None|JoystickButton1|None|10
KeyBinding:Ingame_ConfirmOrAction2|A|Return|None|None|None|JoystickButton0|None|10
KeyBinding:SwitchDirectlyTargetedEntity|Tab|None|None|None|None|JoystickButton11|None|10
KeyBinding:SwitchActiveAbilityBar|None|None|None|None|None|JoystickButton10|None|10
KeyBinding:SwitchActiveAbilityBarReverse|None|None|None|None|None|None|None|10
KeyBinding:SwitchFirstMouseAbilitySlot_UKB2|None|None|None|None|None|None|None|10
KeyBinding:SwitchFirstMouseAbilitySlotReverse_UKB2|None|None|None|None|None|None|None|10
KeyBinding:Ingame_AimUp|None|None|None|None|None|None|Negative5th|5
KeyBinding:Ingame_AimDown|None|None|None|None|None|None|Positive5th|5
KeyBinding:Ingame_AimLeft|None|None|None|None|None|None|Negative4th|5
KeyBinding:Ingame_AimRight|None|None|None|None|None|None|Positive4th|5
KeyBinding:Ingame_UseAbility1|Mouse0|None|None|None|None|JoystickButton2|None|10
KeyBinding:Ingame_UseAbility2|Mouse1|None|None|None|None|JoystickButton3|None|10
KeyBinding:Ingame_UseAbility3|Mouse2|None|None|None|None|JoystickButton4|None|10
KeyBinding:Ingame_UseAbility4|Mouse3|None|None|None|None|JoystickButton5|None|10
KeyBinding:Ingame_UseAbility5|Mouse4|None|None|None|None|JoystickButton6|None|10
KeyBinding:Ingame_UseAbility6|W|None|None|None|None|JoystickButton7|None|10
KeyBinding:Ingame_UseAbility7|R|None|None|None|None|JoystickButton9|None|10
KeyBinding:Ingame_UseAbility8|T|None|None|None|None|None|None|10
KeyBinding:Ingame_UseAbility9|G|None|None|None|None|None|None|10
KeyBinding:Ingame_UseAbility0|V|None|None|None|None|None|None|10
KeyBinding:Ingame_UseAbility11|Mouse0|None|LeftShift|None|None|None|None|10
KeyBinding:Ingame_UseAbility12|Mouse1|None|LeftShift|None|None|None|None|10
KeyBinding:Ingame_UseAbility13|Mouse2|None|LeftShift|None|None|None|None|10
KeyBinding:Ingame_UseAbility14|Mouse3|None|LeftShift|None|None|None|None|10
KeyBinding:Ingame_UseAbility15|Mouse4|None|LeftShift|None|None|None|None|10
KeyBinding:Ingame_UseAbility16|W|None|LeftShift|None|None|None|None|10
KeyBinding:Ingame_UseAbility17|R|None|LeftShift|None|None|None|None|10
KeyBinding:Ingame_UseAbility18|T|None|LeftShift|None|None|None|None|10
KeyBinding:Ingame_UseAbility19|G|None|LeftShift|None|None|None|None|10
KeyBinding:Ingame_UseAbility20|V|None|LeftShift|None|None|None|None|10
KeyBinding:Ingame_UseAbility21|Mouse0|None|LeftAlt|None|None|None|None|10
KeyBinding:Ingame_UseAbility22|Mouse1|None|LeftAlt|None|None|None|None|10
KeyBinding:Ingame_UseAbility23|Mouse2|None|LeftAlt|None|None|None|None|10
KeyBinding:Ingame_UseAbility24|Mouse3|None|LeftAlt|None|None|None|None|10
KeyBinding:Ingame_UseAbility25|Mouse4|None|LeftAlt|None|None|None|None|10
KeyBinding:Ingame_UseAbility26|W|None|LeftAlt|None|None|None|None|10
KeyBinding:Ingame_UseAbility27|R|None|LeftAlt|None|None|None|None|10
KeyBinding:Ingame_UseAbility28|T|None|LeftAlt|None|None|None|None|10
KeyBinding:Ingame_UseAbility29|G|None|LeftAlt|None|None|None|None|10
KeyBinding:Ingame_UseAbility30|V|None|LeftAlt|None|None|None|None|10
KeyBinding:Ingame_MouseAbility1_UKB1|None|None|None|None|None|None|None|10
KeyBinding:Ingame_MouseAbility2_UKB1|None|None|None|None|None|None|None|10
KeyBinding:Ingame_MouseAbility3_UKB1|None|None|None|None|None|None|None|10
KeyBinding:Ingame_MouseAbility4_UKB1|None|None|None|None|None|None|None|10
KeyBinding:Ingame_MouseAbility5_UKB1|None|None|None|None|None|None|None|10
KeyBinding:Ingame_MouseAbility6_UKB1|None|None|None|None|None|None|None|10
KeyBinding:Ingame_MouseAbility7_UKB1|None|None|None|None|None|None|None|10
KeyBinding:OpenMenu_System|Escape|None|None|None|None|JoystickButton8|None|10
KeyBinding:OpenChatPopup_UKB2|I|None|None|None|None|None|None|10
KeyBinding:OpenChunkMap|M|None|None|None|None|None|None|10
KeyBinding:OpenDungeonMap|Comma|None|None|None|None|None|None|10
KeyBinding:OpenRegionMap|Period|None|None|None|None|None|None|10
KeyBinding:Menu_CursorDown|DownArrow|None|None|None|None|None|Down|10
KeyBinding:Menu_CursorUp|UpArrow|None|None|None|None|None|Up|10
KeyBinding:Menu_CursorLeft|LeftArrow|None|None|None|None|None|Left|10
KeyBinding:Menu_CursorRight|RightArrow|None|None|None|None|None|Right|10
KeyBinding:Menu_ConfirmOrAction2|A|Return|None|None|None|JoystickButton0|None|10
KeyBinding:Menu_Cancel|Escape|None|None|None|None|JoystickButton1|None|10
KeyBinding:Menu_SwitchToNextMainTab|Tab|None|None|None|None|JoystickButton3|None|10
KeyBinding:SwitchToGhostMode_UKB1|G|None|LeftControl|None|None|None|None|10
KeyBinding:SwitchToNonGhostMode_UKB1|H|None|LeftControl|None|None|None|None|10
KeyBinding:TriggerAllPointsOfInterest|O|None|None|None|None|None|None|10
KeyBinding:DebugRecreateTestChunk|K|None|LeftControl|None|None|None|None|10
KeyBinding:DebugReloadParticlePatterns|F4|None|LeftControl|None|None|None|None|10
KeyBinding:DebugReloadLanguageFiles|F5|None|LeftControl|None|None|None|None|10
KeyBinding:DebugShowAllRegions|F3|None|LeftControl|None|None|None|None|10
KeyBinding:OpenDebugMenu|L|None|None|None|None|None|None|10
KeyBinding:ResetAimingReticle|U|None|None|None|None|None|None|10
KeyBinding:Ingame_DoLookAhead_UKB1|L|None|None|None|None|None|None|10
KeyBinding:Ingame_Walk|LeftControl|None|None|None|None|None|None|10
KeyBinding:OpenInventory_Usable2|X|I|None|None|None|None|None|10
KeyBinding:OpenInventory_Commodities|K|None|None|None|None|None|None|10
KeyBinding:OpenReference_Planning|P|None|None|None|None|None|None|10
KeyBinding:Visualizer_ShiftWest_UKB1|LeftArrow|None|LeftControl|None|None|None|None|10
KeyBinding:Visualizer_ShiftEast_UKB1|RightArrow|None|LeftControl|None|None|None|None|10
KeyBinding:Visualizer_ShiftUp_UKB1|UpArrow|None|LeftControl|None|None|None|None|10
KeyBinding:Visualizer_ShiftDown_UKB1|DownArrow|None|LeftControl|None|None|None|None|10
KeyBinding:SwapLeftAndRightMouseButtons|None|None|None|None|None|None|None|10
KeyBinding:ForceDropQuantityToAll|LeftControl|None|None|None|None|None|None|10
KeyBinding:OpenInventory_Enchants2|Z|None|None|None|None|None|None|10
KeyBinding:DebugDoMemoryProfilingSample|F9|None|None|None|None|None|None|10
KeyBinding:Ingame_ShowAllRegionLevels|H|None|None|None|None|None|None|10
KeyBinding:Ingame_UseCrate|None|None|None|None|None|None|None|10
KeyBinding:Ingame_UsePlatform|None|None|None|None|None|None|None|10
KeyBinding:Ingame_UseShield|None|None|None|None|None|None|None|10
KeyBinding:Ingame_UseBallOfLight|None|None|None|None|None|None|None|10
KeyBinding:Ingame_UseFlare|None|None|None|None|None|None|None|10
KeyBinding:Ingame_UseLightSnake|None|None|None|None|None|None|None|10
KeyBinding:Ingame_UseFlashOfLight|None|None|None|None|None|None|None|10
Fair warning, this isn't actually supported. Things like casting spells while using menus and modifier keys sticking are expected. Use at your own risk!