We ended up having the infamous issue where the characterization data looks very wonky when using CTRE MAG encoders. This issue is mentioned in the frc docs I think. I made a rogue simulator to see if our trajectory code would have worked in autonomous and it looked amazing. We ordered REV through-bore encoders a few days before the FIRST season was suspended.
Simulation for anyone curious: Simulating Drive Train accurately and Limelight for Autonomous