Are you sure you're installing the new manifold correctly ? I've never seen one that routes the upper line behind the triple tree bottom clamp. It should route up between the front of the bottom clamp and the nacelle and the hose would exit the top of the nacelle next to the right handlebar clamp then to the master cylinder.
Looking at the bottom picture of the new maniflod it looks like that would work.
Disclaimer : Don't believe anything I say unless you are absolutely sure that I know what I'm talking about .