Diodes in input protection circuits
D2 is a bipolar TVS. It's to protect against large positive or negative transients by shunting them out. There is no series impedance so it won't necessarily do well against high current or high energy transients.
C9 is probably not necessary. There is a lot of capacitance in Q3's gate and some in the zener. It might help if there was some possibility of the input voltage being suddenly reversed after being in the correct polarity, in which case the MOSFET could conduct  a
large negative current for maybe hundreds of microseconds.
D4 isolates the 7805 for some reason. Possibly to do with whatever Vbb is used for (backup battery charging?). It prevents a short on Vbb from suddenly reducing the input voltage to the regulator, though that's usually not a problem with only 5V. Also if a negative transient makes it through the MOSFET it protects the 7805. The electrolytic capacitors would probably be okay, assuming they're not tantalums.

You'd want to pick the MOSFET based on the minimum input voltage, which might be the voltage during cranking or something like that, and the maximum current and allowable voltage drop. If the input voltage can fall to (say) 7V then the MOSFET needs to be fully on at 7V. It also must be able to block the highest negative input voltage that might be applied. For that you'd look at the TVS specification at the maximum negative input current.
If you're not so concerned about low voltage drop, you can replace the MOSFET and the three associated parts with a 1N4007 which will withstand -1kV and is smaller, cheaper and likely more reliable.
TVS selection- you need to protect the MOSFET against breakdown when blocking and the 7805 against the 35V or so that it can deal with - so the voltage across it should not exceed those when subjected to the maximum current that you are expected to protect against. It also needs to not join the choir invisible itself, so maximum energy of the expected transient is a consideration. You also must ensure the TVS does not conduct with the maximum applied (non-transient) voltage (or it will quickly die).
Note that this circuit does not have a lot of bulk filtering (44uF is not much) so if the input voltage falls below the dropout the output voltages will go out of regulation rather quickly (milliseconds).