AFAIK the only realistic methods that can scan a head port directly would involve a laser or structured light scanner on a CMM arm. Both are way out of my price range, even to rent. That sort of setup would literally cost more than my house lol! But watch in 5 years they'll be $500 on fleabay.
The cheaper and more common way is to scan a casting, thats what I did with the swirl intake port and CC I scanned.
For references I also cast the head gasket and intake manifold gasket surfaces. The valve guide gets cast along with the machined conical bowl. So all those things let you align it in space correctly.
For your ports I would imagine the same process I used for the scanning I did would work just fine.
Did you see my scanning thread? It shows everything I did from silicone to CNCing a feature in the CC based on scan geometry.
http://www.turbododge.com/forums/f32...-our-head.html
What are your goals for scanning? Do you want to just have an accurate record of your work in 3 dimensions or would you want to go all the way to trying to duplicate them in CNC?
The chinese 3" rotary table got here today but it has a brass ring gear so I dont think its up to the torque required to turn a fully-stocked valvetrain. But it would probably do the job of the big rotary I was using for cam measuring on the bench. Things are ripe for making a little fixture to hold the rotary table in place and also the dial indicators so its set-and-forget and measure any cam with zilch setup. If one were to get a cheapo digital dial indicator and hook up a stepper motor you could make an electronic/computerized cam scanner which could give you the entire profile. Although its super easy to get really close by making measurements every 5 degrees or so manually.