This program is only accurate around the values normally found with Citroën A-types.
Very powerfull or heavy cars will give inaccurate figures.
The acceleration only depends on the engine torque and weight of the car.
To also include gearbox and tyres the torque curve of an engine has to be known.
This is not within the scope of this program.
The topspeed given is a theoretical top speed.
This is the topspeed possible with your car body (and the aerodynamic drag resulting from it) and engine power.
The gearbox advice is just checking to see if your car will reach your theoretical topspeed at the engine maximum power rpm.