Thank you all for the fantastic advice! I'm going to take a hybrid approach for my engineering resume:
Group skills by category (design, analysis, manufacturing, etc.)
Include all relevant skills but bold/highlight advanced ones
Create a master list but customize emphasis for each application
Most importantly, back up advanced skills with specific examples in my work experience section
This seems like the best way to be comprehensive while still being honest about my proficiency levels. I really appreciate all your insights!