I've used lithium batteries in most of my bikes. They seem to work fine but maybe its just a problem waiting to happen.
On my 56 black Huntmaster I've oppened up the battery case and removed the cells. It seems that even the small case still has a lot of empty space inside. The flat cells are much smaller then the case. I put these cells in the bottom of my black rubber case leaving room for all my electrical stuff keeping it all out of the damp. I manged to get my electronic igniction modual and a relay in.