I only have one grade when I go to school. This doesn't make sense.

I think there could be a way for a sufficiently adept scripter to create the illusion of having multiple classes. The vanilla "grade" would simply be re-worked into a "GPA," which would be dependent on the green bar on the right being filled up as usual. However, the green bar would not be filled up simply by "working hard," but rather, based on the grades you receive in your "hidden" classes, whose grades you can check

For example, English and History would be separate classes. Having the "Bookworm" trait and a decent writing skill would improve the rate at which your grades improve.
The Math and Science classes would get a boost to its rating if you're a genius and have a high logic skill. With UL installed, the science skill would also boost your rating.
P.E. class (physical education) would be based on your athletics and (if you have WA installed) martial arts skills, as well as having the athletic skill.
Art would be based on your artistic & virtuoso traits, as well as your kills in painting, street art, sculpting, and whatever musical instruments you have access to, given your EPs.

With sufficient skills and traits (usually skill levels of five or more, seven without the traits), you should be able to get straight As no matter what you do in school, assuming you don't just cut class altogether.

Anyone know where I could find a mod even remotely similar to what I have in mind?

I like this idea. Too bad there is no answers - I'm afraid it doesn't exist because it sounds complicated and often complicated things don't.