I simply don’t give grades. We only grade the “easily-testable” subjects–math, science, Latin. Everything else I write a description of the course explaining our mastery approach, explaining the work involved, and stating that the child met the goals of the course.
Remember, this is YOUR high school. You can do it how you want. Another thing you might want to consider if you use CM methods is the possibility of writing course descriptions that cover several years–for example, instead of doing “9th grade history” “10th grade history” etc, I give one credit for American history and one credit for World history. I organize my transcripts by subject instead of by year.
There are a number of resources out there to help with all this.