www.makemkv.com

Is there a way to get more diag data from makemkv or VLC when using direct playback with VLC?

Something like what #####.mpls file is in use
or
segment map

anything that would provide a direction.

If you're hoping for something to tell you which play list is the correct one to rip, probably not to that level. You can turn on debug logging in MakeMKV, and open the Information screen in VLC, but that is about the maximum.