I'd leave the master cylinder where it is and put a scoop or bulge over it. I was planning to use the plastic packaging from an Easter egg as a template to make a blister if my servo had been too high. It won't look odd, all the old racing cars had them.
As for lowering the suspension. In the words of a well known sports clothing manufacturer's advertising department, Just Do It! Mine's very low and it sailed over a bunch of speed bumps on the way to the DVLA office in Peterborough without any grounding issues. Take a look at the clearance under a modern car - the Saab 9-3 I recently parted with only had 100mm ground clearance, which is about the same as I have in the Spyder.
Looking forward to seeing your car progress, I'll put a fiver on Easter 2013 as a finish date. Oh, but I want odds of 500,000 to one...
