Thook- glad you like my project. CX refit is definitely a good way to add some new life into a nice old frame. Good luck with your conversion.
CX tubulars are lighter than clinchers, you can run less pressure in them for better grip/traction/handeling and they are much less prone to snake-bite pinch flats. I doubt that they are any more prone to puncture flats than clinchers of similar construction. That said, CX tubulars are really expensive and probably not worth the additional cost and glue job maintenance if you are not racing on them.
I did drill out the stem for the cable stop. It is a really beefy solid cast stem, cant imagine the small hole will be a problem. Just dont try it with a hollow stem