If you haven't put the headers on you might want to re-route the spark plug wires. While running them under manifolds is common, they'd cook under headers.
I'm curious why you are concerned with changing the master cylinder to a more accurate unit, (although the power booster looks a litte anemic on the one on the right), but don't seem to care about running the more visible ignition wires correctly? Seems if you are upgrading some parts you'd want the rest to be accurate too. Maybe I'm missing something.
It's not like it costs more to do it correctly...