Woo hoo! We have success on the exhaust calculations, although I still have a couple of questions. I found the exhaust opening number for the 400F from my Clymer manual (35 degrees before BDC) so used that. In addition PJ kindly sent me a link to the BG Tuning Manual which showed me some ways to calculate the exhaust measurements in metric (which is where I suspect I was coming undone before).
I had to estimate the revs the bike made max power, not sure if I had to do this based on the current max power point of the bike or if I could nominate an ideal RPM. I went the latter and put in 8,000 RPM (assuming this would give plenty of power in that point where you overtake). If those that know what they are doing could feedback on this point I would be highly appreciative.
All in all the measurements appear to be spot on (and the book is very easy to follow):
I built a spreadsheet for the calculations which I am happy to share of anyone wants it. Just enter a few items and the rest works itself out. Also most of the info I read (Sonrier's excellent Build a Functional Cafe Racer and the BG Tuning Book) talk about two ways to build a header for a 4 cylinder. 4-1 for max power or 4-2-1 or a broader spread of power, I am leaning to the 4-2-1 for street use as I would assume it would provide a greater sense of power and useability, however not if it really reduces the "hit", to those that know, please advise me on this one.
So the final results are:
Header length: 24.4"
Header diameter: 1.09"
Secondary header length: 24.4"
Secondary header diameter: 2.04"