Whenever I turn into a lich with lichcraft I have clipping issues with the skull. I can see it in first person view and it's really annoying. I tried changing the Fneardistance or whatever in the INI file, but it did nothing to solve the issue. Is there something I can do in the construction set to fix this?

I know that the "3rd Person Animations in 1st Person View" resources used by DR6 causes clipping. The stand-alone mod did as well. That could be your problem.

is there a way to fix this or do I just have to disable deadly reflex 6?

IIRC, That aspect is built into DR6, and not an optional Esp file. So that would mean disabling DR6 to prevent the clipping.