There are script functions that set the bike's speed/max speed/acceleration, presumably used with the boost pads. You could probably just set some globals for having mods installed and then add a multiplier to the speed/acceleration based on a check of those.
Edit: For example, when you hit a boost pad it checks the global for what gear you're in (MIN_RACE_GEAR) and, if you aren't in 5th gear, applies:
SWMG_SetPlayerAccelerationPerSecond(SWMG_GetPlayerAccelerationPerSecond() * 1.1);
SWMG_SetPlayerSpeed(SWMG_GetPlayerSpeed() * 1.05);
Similarly, if you hit an obstacle, it applies:
SWMG_SetPlayerSpeed(SWMG_GetPlayerSpeed() * 0.7);
For the purposes of mods, you wouldn't want to directly affect the current speed, so you'd likely stick to starting with:
SWMG_SetPlayerMinSpeed
SWMG_SetPlayerMaxSpeed
at the beginning of a race. Additionally you might also want to increase the performance of boost pads and/or reduce the effect of obstacles, depending on the mods installed. Or you could even do the opposite, decrease the effectiveness of boosts and increase the penalty of hitting obstacles, if you wanted certain mods to have drawbacks as well as bonuses. Or some combination thereof (e.g. a "Heavy Plating" mod that reduces max speed and the benefits of boost pads, but lets you plow through obstacles with a minimal reduction in speed).