FWIW, I recently did the top end on my KTM. I had had it replated by US Chrome almost 2 years ago, so I emailed them to find out their recommendation. Their response was that unless it was a "diamond hone", and if it was in other wise good shape, to only dip it in a 20% Muratic acid solution and a bit of scotch bright clean up. That is exactly what I did - time will tell if it was the right way to go or not.
One thing that did impress me though, is my top end had at least 2500 miles (or more - maybe closer to 3,000) of riding on it, and it looked as good as the day I got it back from US Chrome!