Update: I have made another post with better instructions and a new build.
Another little update to the changes I made to multiclutch.
I realised I could make the input manager load for all applications by using a * target application identifier for the SIMBL properties (so that is being used now).
I have also built the input manager as a universal application, so that it will now work for 32 bit and 64 bit applications, so the old input manager for MultiClutch in /Library/InputManagers should not be necessary anymore.
I have put up the build here:
Multiclutch Universal Build
Let me know how it goes!