If your next bit is getting it all working when you change into gear, I''d say a little logical reorganization is in order (unless you got there ahead of me, of course).
The way I''d do it is break up the system logically into a set of components. Each component has an input shaft and an output shaft. The output shaft of one component is connected to the input shaft of the next by a coupling, which has various parameters (maximum torque transmitted before slippage, maximum RPM, etc.) which determine how the input energy is transferred. Then you simply build the drivetrain of your car, in software. Like:
(engine) -> (clutch coupling) -> (gearbox) -> (simple coupling) -> (differential) -> (simple coupling) -> (wheels)
So your engine is a free standing unit. All it knows about is its inputs (throttle, manifold pressure, fuel pressure, as complex or simple as you like) and its output (a single shaft, spinning at X rpm). For the simulation to be physically realistic I''d model the engine as a rotating mass attached to its output shaft, with some drag on it to simulate internal friction and a magical torque force applied to simulate actual engine power generation. The clutch is a simple system that transmits x% of its input torque to its output torque, and vice versa - you probably don''t have to worry about modelling clutch rotating mass etc. because clutches don''t weigh that much. The gearbox converts input torque to output torque based on its current gear ratio.
When you get to the wheels, that''s when it gets interesting. You need to calculate the torque on the wheels by taking into account (a) the torque applied by the axles, and (b) the frictional force on the road. It''d probably be wise to get someone who''s done engineering dynamics more recently than I to help you out from this point on...
Best way to learn how to do this stuff is get a kinematics/dynamics textbook out of a library and work through it. Learn how to use free body diagrams, and every problem becomes the simple (heh right) matter of dividing the system up into appropriate free bodies.
