There is no NavXIO abstraction so currently the pigeon one is being used (we don't have a pigeon). You can find another team who uses Advantage Kit with a NavX and use their abstraction or make your own
The Spark Max abstractions are used instead of the Talon ones in the robot container switch statement. We have krakens controlled via TalonFX motor controllers. Additionally, the configs for TalonFX are set for L2 swerve when we use L3+, look at this year's 2024-Robot repo for the correct gear ratios.
The ModuleIOSim used for simulating the robot likely does not have the correct values (gearing, MOI, motor, etc). I recommend looking for another team with L3+ Kraken Swerve who also uses Advantage Kit and take their configs