Without knowing for certain the overall mechanical design, I can't tell whether the code is really proper.
For instance, let's say your linear actuators aren't able to be back-driven by the spring pressure of the fuel pedal (or throttle) and the brake mechanism. What happens if the linear actuator's power cable breaks or disconnects in some manner?
For that matter - where in your code are you testing for that possibility (and then going into e-stop mode when it occurs)? I don't see anything about that.
What you are building is the equivalent of a large-scale robot, that happens to have a cargo of a man in it, taking and acting on commands that man gives via some set of controls (joystick or otherwise).
I have some limited experience with working on and refurbishing mobility scooters and wheelchairs. While they may look like simple devices, they are anything but. In fact - they themselves are robots of a sort. As such, they are built with safety first and foremost up front. If the battery voltage varies by any amount, if any potentiometer or other control isn't outputing the proper resistance, voltage, or other signal - if the user isn't sitting in the chair...all of these instantly shuts the machine down, and triggers an error.
You need to design this into your system first. In fact, I would scrap the code you have already written, and then think very carefully about how you intend to modify the vehicle to work with the automated control system, along with what modifications (mechanical or electrical) you can introduce to implement a fail-safe system. Try to think of any or all options; overspeed, roll and pitch angle, loss of steering or braking, stuck accelerator, etc. Try to think of ways to bring the system to a halt instantly - or as quickly as possible - in each scenario. Then try to think of ways to do this with the the Arduino controlling that system.
Also think of ways to have the system detect if a controller malfunctions. Be sure to implement an emergency stop button (or multiple buttons! - and use a real e-stop button that can't be easily reset after it is activated - like those used in factories, etc) - and perhaps implement it in some manner that is electrically based, or has a component separate from the code/Arduino (in case the Arduino fails, for instance!). One way, for instance, would be if the button is pressed, it cuts off power, which causes a valve to close to cut fuel off from the engine, and maybe activates the brake using an electro-mechanical system of some sort.
Once you have come up with a complete plan - go over it with your friend. Go over it with other people. Try to have them pick it apart, see if there are any obvious weak spots. Then fix those spots. Then - take a month off away from the whole system (and don't think about it at all!). Then come back, look it over, and see if you spot anything obvious you missed. You won't necessarily catch everything, and you may not be able to make it perfect (since you are working with a machine that wasn't meant to be modified in such a manner), but you can get very, very close.
You might look into and/or talk to companies who modify vans and other automobiles for disabled people to use, to find out what they do for safety purposes. It couldn't hurt to at least try.
Ultimately, you need to be designing this system from the ground up for safety; if you aren't doing this, you'll be doing your friend a disservice.