Hello,
I recently downloaded MadamDoofie's Minimum Wage/Realistic Earnings for lower wages, which works great! However, after my sim earned an A grade in their degree, they made too much money -- almost §2000/hr! I took the mod out and the wage lowered a few hundred but still too much.

So, I'm wondering if there's a setting in Retuner to lower wages with special consideration of Degree Bonuses?

I'm running into the same issue. I'm trying to play with reduced salaries and I've done my own edits to the Careers xml to achieve this. However, what I didn't take into account was the pay bonus you get for completing a degree (my sim is an A student). For future reference, if anyone wants to edit these values they are in the Career xml (Instance: 0xDC0D299F04BB3773). If using Retuner, the path is Settings > General > By Tunable XML > Sims3.Gameplay.Careers > Career and then you want to edit the values in the four kCareerBonusesForDegree... menus.