You _can_ go closer to the head on the intake side; reason being that you can raise the intake port to the point that it doesn't interfere with the ring, and this will effectively increase your port size/flow without altering duration, or making it wide enough to worry about snagging the piston. I do this to all of my cylinders.
I agree, cut your piston skirt 2-3mm; since you've got reeds, intake duration isn't as critical as on a piston-port kit. This is a Tomos Airsal, yeah?
That looks like a good starting point for a mild port job. Do that, do it well, chamfer the ports, and run it for about a week to think about what you want to do differently. Have fun with it!