Hmm, okay. I only went up about 3mm on the exhaust, but I milled about 2mm off the top of the cylinder, then ported using that new height as zero; so my effective raise was 5mm on the exhaust, 2mm on the transfers. The cylinder is spaced from the bottom to match my new deck height, and I planed my head to maintain squish clearance. I shaped my exhaust port like that too, except not too prominent. My exhaust port was right at 30mm wide, from the window to the port, to match the Simonini header. For the intake, I went down about 1.5mm, didn't widen it too much. That's what keeps my power curve smooth; but I know I'm losing power because of it. Case induction will fix all that right up, though.
I went pretty radical with my piston on the mill, though. I connected both sets of holes, and lowered them about 2mm. This really helped the 6p with my loop scavenge, you should see the combustion patterns on my piston.