Is there a particular reason why you want to change to negative ground? I can see the advantage if you have plans to use some polarity specific LED's, but otherwise I don't see the need.
Whatever you do, either keep the color codes the same (at least red for positive and white or black for negative) or include a clear copy of the wiring diagram so someone other than yourself can follow your logic. I would also suggest a clear label on the battery box that the bike has been converted to negative ground.
Maybe it's 30+ years with British bikes, but when I look at a component on one I expect it to be positive ground and a red wire should be a ground. I don't like to be surprised!
As for the capacitor, I generally eliminate them when an EI is present. If they are in good shape it will start with a low or no battery, but they are often 40 years old and leak. Then they serve no purpose at all.